Annotation of Secretariat and Hydrus, two DJ cluster phages isolated on Gordonia rubripertincta.

Secretariat and Hydrus are phages grouped into the DJ cluster that were isolated on Gordonia rubripertincta NRRL B-16540. The phages have 75% nucleotide identity and share 73% gene content. Secretariat has a genome with 84 predicted genes, while Hydrus has 91 predicted genes and can also infect Gordonia terrae 3612.

Isolation and Annotation of Azira, a CT Cluster Phage That Infects Gordonia rubripertincta.

Azira is a CT cluster actinobacteriophage that infects Gordonia rubripertincta NRRL B-16540. The genome contains 67 predicted protein coding genes, of which 31 have a putative function. Azira has a lysis cassette encoding two endolysins and three transmembrane proteins. Azira contains four genes predicted to encode enzymes involved in thymine synthesis.

Prediction of the Values of CRP, eGFR, and Hemoglobin in the Follow-Up of Renal Cell Carcinoma Patients after (Cryo)Surgery Using Machine Learning Algorithms.

BACKGROUND: Artificial intelligence can support clinical decisions by predictive modeling. Using patient-specific characteristics, models may predict the course of clinical parameters, thus guiding monitoring approaches for the individual patient. Here, we present prediction models for inflammation and for the course of renal function and hemoglobin (Hb) in renal cell carcinoma patients after (cryo)surgery. METHODS: Using random forest machine learning in a longitudinal value-based healthcare data set (n = 86) of renal cell carcinoma patients, prediction models were established and optimized using random and grid searches. Data were split into a training and test set in a 70:30 ratio. Inflammation was predicted for a single timepoint, whereas for renal function estimated glomerular filtration rate (eGFR) and Hb time course prediction was performed. RESULTS: Whereas the last Hb and eGFR values before (cryo)surgery were the main basis for the course of Hb and renal function, age and several time frame features also contributed significantly. For eGFR, the type of (cryo)surgery was also a main predicting feature, and for Hb, tumor location, and body mass index were important predictors. With regard to prediction of inflammation no feature was markedly prominent. Inflammation prediction was based on a combination of patient characteristics, physiological parameters, and time frame features. CONCLUSIONS: This study provided interesting insights into factors influencing complications and recovery in individual renal cell carcinoma patients. The established prediction models provide the basis for development of clinical decision support tools for selection and timing of laboratory analyses after (cryo)surgery, thus contributing to quality and efficiency of care.

Evolution of the grass leaf by primordium extension and petiole-lamina remodeling.

The sheathing leaf found in grasses and other monocots is an evolutionary innovation, yet its origin has been a subject of long-standing debate. Here, we revisit the problem in the light of developmental genetics and computational modeling. We show that the sheathing leaf likely arose through WOX-gene-dependent extension of a primordial zone straddling concentric domains around the shoot apex. Patterned growth within this zone, oriented by two polarity fields, accounts for wild-type, mutant and mosaic grass leaf development, whereas zone contraction and growth remodeling accounts for eudicot leaf development. In contrast to the prevailing view, our results suggest that the sheath derives from petiole, whereas the blade derives from the lamina of the eudicot leaf, consistent with homologies proposed in the 19th century.

Norwich COVID-19 testing initiative pilot: evaluating the feasibility of asymptomatic testing on a university campus.

BACKGROUND: There is a high prevalence of COVID-19 in university-age students, who are returning to campuses. There is little evidence regarding the feasibility of universal, asymptomatic testing to help control outbreaks in this population. This study aimed to pilot mass COVID-19 testing on a university research park, to assess the feasibility and acceptability of scaling up testing to all staff and students. METHODS: This was a cross-sectional feasibility study on a university research park in the East of England. All staff and students (5625) were eligible to participate. All participants were offered four PCR swabs, which they self-administered over two weeks. Outcome measures included uptake, drop-out rate, positivity rates, participant acceptability measures, laboratory processing measures, data collection and management measures. RESULTS: 798 (76%) of 1053 who registered provided at least one swab; 687 (86%) provided all four; 792 (99%) of 798 who submitted at least one swab had all negative results and 6 participants had one inconclusive result. There were no positive results. 458 (57%) of 798 participants responded to a post-testing survey, demonstrating a mean acceptability score of 4.51/5, with five being the most positive. CONCLUSIONS: Repeated self-testing for COVID-19 using PCR is feasible and acceptable to a university population.

Markers of eosinophilic inflammation and risk prediction in patients with coronary artery disease.

BACKGROUND: The eotaxin family comprises three distinct peptides (eotaxin, eotaxin-2 and eotaxin-3) which have been implicated in eosinophilic inflammation. In vitro and clinical studies suggest that eotaxins could play a role in vascular inflammation, but no data are available on their prognostic significance in patients with angiographically documented coronary artery disease (CAD). MATERIALS AND METHODS: Baseline plasma samples were obtained from 1014 patients with documented CAD. We tested the predictive effect of markers of eosinophilic inflammation and C-reactive protein (CRP) on death from cardiovascular causes and nonfatal myocardial infarction over a 2.7-4.1-year follow-up period. RESULTS: Unexpectedly, lower eotaxin-3 concentrations were observed in patients with adverse cardiovascular events, whereas both eotaxin and eotaxin-2 showed no association with risk. After adjustment for most potential confounders, patients in the upper-quartile of eotaxin-3 levels had a 0.42 hazard-ratio (95% CI, 0.29-0.61, P < 0.001) for adverse events compared with subjects in the lower-quartile. The highest risk of future cardiovascular events was observed in subjects with combined elevation of CRP and reduction of eotaxin-3; 4.4 hazard-ratio (95% CI, 2.1-9.5, P < 0.001). Importantly, receiver-operating-characteristic curves analysis suggested a superior prognostic value of eotaxin-3 compared with CRP for predicting cardiac events in patients with CAD. CONCLUSIONS: Low levels of eotaxin-3 are an independent predictor of future adverse cardiovascular events in patients with CAD and may be useful for risk stratification.

Ancient asymmetries in the evolution of flowers.

Dorsoventral asymmetry in flowers is thought to have evolved many times independently as a specialized adaptation to animal pollinators. To understand how such a complex trait could have arisen repeatedly, we have compared the expression of a gene controlling dorsoventral asymmetry in Antirrhinum with its counterpart in Arabidopsis, a distantly related species with radially symmetrical flowers. We found that the Arabidopsis gene is expressed asymmetrically in floral meristems, even though they are destined to form symmetrical flowers. This suggests that, although the flowers of the common ancestor were probably radially symmetrical, they may have had an incipient asymmetry, evident at the level of early gene activity, which could have been recruited many times during evolution to generate asymmetric flowers.

Goethe and the ABC model of flower development.

About 10 years ago, the ABC model for the genetic control of flower development was proposed. This model was initially based on the analysis of mutant flowers but has subsequently been confirmed by molecular analysis. This paper describes the 200-year history behind this model, from the late 18th century when Goethe arrived at his idea of plant metamorphosis, to the genetic studies on flower mutants carried out on Arabidopsis and Antirrhinum in the late 20th century.

The gene fimbriata interacts non-cell autonomously with floral regulatory genes.

In Antirrhinum majus, one proposed role of the gene fimbriata (fim) is as a mediator between the floral meristem identify gene floricaula (flo) and floral organ identity genes such as deficiens (def) and plena (ple). The mechanism of fim activity is probably unique as, while the other genes in the hierarchy are thought to be transcription factors, fim is thought to target proteins to a ubiquitin-mediated destruction pathway. Both flo and def have been shown to act non-cell autonomously. We tested the hypotheses that (i) fim acts in a non-cell autonomous manner; and (ii) non-cell autonomy of flo might be through activation and subsequent non-cell autonomous activity of fim. Plants bearing an unstable fim allele were monitored for revertant shoots. Analysis of fim RNA expression in plants derived from revertant shoots, and segregation of revertant phenotype in progeny from revertant plants, indicated that all were periclinal chimeras with wild-type fim expression only in subepidermal layers. Despite the absence of fim in the epidermal layer, expression of downstream genes was normal, suggesting non-cell autonomous activity of fim. Subsequently, we tested the hypothesis that fim is the mediator of flo non-cell autonomy by examining fim expression in flo periclinal chimeras. In these chimeras, fim is activated in cells where flo is not expressed, indicating that fim cannot be the sole mediator of flo non-cell autonomy.

The expression of D-cyclin genes defines distinct developmental zones in snapdragon apical meristems and is locally regulated by the Cycloidea gene.

Three D-cyclin genes are expressed in the apical meristems of snapdragon (Antirrhinum majus). The cyclin D1 and D3b genes are expressed throughout meristems, whereas cyclin D3a is restricted to the peripheral region of the meristem, especially the organ primordia. During floral development, cyclin D3b expression is: (a) locally modulated in the cells immediately surrounding the base of organ primordia, defining a zone between lateral organs that may act as a developmental boundary; (b) locally modulated in the ventral petals during petal folding; and (c) is specifically repressed in the dorsal stamen by the cycloidea gene. Expression of both cyclin D3 genes is reduced prior to the cessation of cell cycle activity, as judged by histone H4 expression. Expression of all three D-cyclin genes is modulated by factors that regulate plant growth, particularly sucrose and cytokinin. These observations may provide a molecular basis for understanding the local regulation of cell proliferation during plant growth and development.

Control of organ asymmetry in flowers of Antirrhinum.

Organ asymmetry is thought to have evolved many times independently in plants. In Antirrhinum, asymmetry of the flower and its component organs requires cyc and dich gene activity. We show that, like cyc, the dich gene encodes a product belonging to the TCP family of DNA-binding proteins that is first expressed in the dorsal domain of early floral meristems. However, whereas cyc continues to be expressed throughout dorsal regions, expression of dich eventually becomes restricted to the most dorsal half of each dorsal petal. This correlates with the effects of dich mutations and ectopic cyc expression on petal shape, providing an indication that plant organ asymmetry can reflect subdomains of gene activity. Taken together, the results indicate that plant organ asymmetry can arise through a series of steps during which early asymmetry in the developing meristem is progressively built upon.

An epigenetic mutation responsible for natural variation in floral symmetry.

Although there have been many molecular studies of morphological mutants generated in the laboratory, it is unclear how these are related to mutants in natural populations, where the constraints of natural selection and breeding structure are quite different. Here we characterize a naturally occurring mutant of Linaria vulgaris, originally described more than 250 years ago by Linnaeus, in which the fundamental symmetry of the flower is changed from bilateral to radial. We show that the mutant carries a defect in Lcyc, a homologue of the cycloidea gene which controls dorsoventral asymmetry in Antirrhinum. The Lcyc gene is extensively methylated and transcriptionally silent in the mutant. This modification is heritable and co-segregates with the mutant phenotype. Occasionally the mutant reverts phenotypically during somatic development, correlating with demethylation of Lcyc and restoration of gene expression. It is surprising that the first natural morphological mutant to be characterized should trace to methylation, given the rarity of this mutational mechanism in the laboratory. This indicates that epigenetic mutations may play a more significant role in evolution than has hitherto been suspected.

Can MRI replace a second look operation in cholesteatoma surgery?

The purpose of this paper is to investigate whether a magnetic resonance imaging (MRI) examination of the petrous bones could replace the conventional second look surgical procedure when a canal wall up tympanoplasty procedure has been performed during the first look surgery. Eighteen patients were examined with MRI prior to a second look surgical procedure. MRI was performed on a 1.5 T superconducting system. T2 weighted images before contrast and T1 weighted images after contrast (gadopentate dimeglumine) were obtained. Imaging results were compared with surgical findings. The poor radiosurgical correlation (50% and 61% after re-evaluation) suggests that, at the present time, MRI is not a valid alternative to a second look surgical intervention in the case of cholesteatoma treated by canal wall up tympanoplasty. In our study, MRI was not capable of differentiating small pearls of residual cholesteatoma from surrounding scar tissue.

The TCP domain: a motif found in proteins regulating plant growth and development.

The cycloidea (cyc) and teosinte branched 1 (tb1) genes code for structurally related proteins implicated in the evolution of key morphological traits. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. To address this problem, we have analysed the predicted secondary structure of regions conserved between CYC and TB1, and looked for related proteins of known function. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This indicates that the conserved domain most probably defines a new family of transcription factors, which we have termed the TCP family after its first characterised members (TB1, CYC and PCFs). Other plant proteins of unknown function also belong to this family. We have studied two of these in Arabidopsis and have shown that they are expressed in rapidly growing floral primordia. This, together with the proposed involvement of cyc and tb1 in influencing meristem growth, suggests that many members of the TCP family may affect cell division. Some of these genes may have been recruited during plant evolution to generate new morphological traits.

The processing of secretogranin II in the peripheral nervous system: release of secretoneurin from porcine sympathetic nerve terminals.

The distribution of secretoneurin (SN), a peptide derived from secretogranin II (SgII), in the coeliac ganglion, the splenic nerve and the spleen was examined by immunohistochemistry. In the ganglion, SN immunoreactivity (IR) was unevenly distributed. Positive nerve terminals densely surrounded some postganglionic perikarya in which also intense SN-IR was present. In the crushed splenic nerves, intense immunoreactivities appeared proximal (but to a less extent also distal) to the crush of the nerve. Analysis by cytofluorimetric scanning (CFS) demonstrated that SN-IR and neuropeptide Y immunoreactivity (NPY-IR) were predominant in the axons proximal to the crush representing anterogradely transported components. Using radioimmunoassay (RIA) we demonstrated that upon electrical stimulation (10 Hz, 1 min) of the splenic nerve, significant amounts of SN-IR (64.2+/-2.3 fmol) were released together with NA (4. 1x106+/-0.2 fmol) and NPY (330.0+/-7.2 fmol) from the isolated perfused porcine spleen. To evaluate the processing of SgII in sympathetic neurons, boiled tissue extracts (coeliac ganglia and splenic nerve) and boiled spleen perfusate (used as a suitable source for vesicle derived peptides) were analysed by gel filtration chromatography followed by SN-RIA. In all cases immunoreactivity was present solely as SN, indicating that SgII was fully processed to the free peptide. The evidence that SN is transported to the nerve terminals and is released from the porcine spleen upon nerve stimulation, suggests that it may modulate adrenergic neurotransmission and may also play a role in the neuroimmune communication.

Separation of shoot and floral identity in Arabidopsis.

The overall morphology of an Arabidopsis plant depends on the behaviour of its meristems. Meristems derived from the shoot apex can develop into either shoots or flowers. The distinction between these alternative fates requires separation between the function of floral meristem identity genes and the function of an antagonistic group of genes, which includes TERMINAL FLOWER 1. We show that the activities of these genes are restricted to separate domains of the shoot apex by different mechanisms. Meristem identity genes, such as LEAFY, APETALA 1 and CAULIFLOWER, prevent TERMINAL FLOWER 1 transcription in floral meristems on the apex periphery. TERMINAL FLOWER 1, in turn, can inhibit the activity of meristem identity genes at the centre of the shoot apex in two ways; first by delaying their upregulation, and second, by preventing the meristem from responding to LEAFY or APETALA 1. We suggest that the wild-type pattern of TERMINAL FLOWER 1 and floral meristem identity gene expression depends on the relative timing of their upregulation.

The Antirrhinum ERG gene encodes a protein related to bacterial small GTPases and is required for embryonic viability.

Small GTPases have diverse roles in animals and yeast, including signal transduction, regulation of secretion, organisation of the cytoskeleton, and control of cell division. Similar GTPases have also been found in bacteria, such as the Escherichia coli GTPase ERA, which is involved in regulating metabolism and cell division [1,2]. Many small GTPases have been cloned from plants but their functional analysis has largely been limited to complementation of mutations in corresponding yeast genes, and antisense experiments which have implicated these proteins in processes such as root nodulation [3,4]. No mutations in plant GTPases have been reported, and thus their true importance in plant growth and development is unknown. Here we report the isolation of a gene from Antirrhinum majus encoding a protein from an entirely novel class of eukaryotic GTPases showing strongest similarity to the prokaryotic protein ERA. We have named this gene ERG (for ERA-related GTPase). The ERG gene is expressed in dividing or metabolically active cells. We generated a deletion allele of ERG by site-selected transposon mutagenesis and have shown that seeds containing embryos and endosperm homozygous for this deletion arrest soon after fertilisation. We conclude that ERG has a crucial role in plant growth and development, possibly by influencing mitochondrial division.

Central sleep apnea after interrupting longterm acetazolamide therapy.

One month administration of acetazolamide (ACET) (at sea level) improves periodic breathing and decreases the number of central apneas (CA) (De Backer et al., 1995 Am. J. Respir. Crit. Care Med. 151, 87-91) in nonhypercapnic central apnea syndrome. It remains unclear whether cessation of therapy would provoke recurrence of symptoms. In the present study we evaluated the number of CA after 1 and 6 months interruption of ACET therapy. Eight patients with central sleep apnea were included [central apnea index (CAI) > 5 or apnea and hypopnea index (AHI) > 10 and obstructive apnea index (OAI) < 5]. Polysomnography was repeated once after 1 month treatment (N2), after 1 month off treatment (N3) and after 6 months off treatment. CAI (25 +/- 10 at N1) decreased during N2 (4 +/- 2) and N3 (5 +/- 3) and remained low after N4 (3 +/- 1). However an increase in the number of obstructive apneas and central hypopneas could be observed together with a shift from central apnea to hypopnea after N4. Maybe ACET induces a long lasting resetting of the CO2 threshold which is still present after interruption of the therapy.

Control of floral homeotic gene expression and organ morphogenesis in Antirrhinum.

The development of reproductive organs in Antirrhinum depends on the expression of an organ identity gene, plena, in the central domain of the floral meristem. To investigate the mechanism by which plena is regulated, we have characterised three mutants in which the pattern of plena expression is altered. In polypetala mutants, expression of plena is greatly reduced, resulting in a proliferation of petals in place of reproductive organs. In addition, polypetala mutants exhibit an altered pattern of floral organ initiation, quite unlike that seen in loss-of-function plena mutants. This suggests that polypetala normally has two roles in flower development: regulation of plena and control of organ primordia formation. In fistulata mutants, plena is ectopically expressed in the distal domain of petal primordia, resulting in the production of anther-like tissue in place of petal lobes. Flowers of fistulata mutants also show a reduced rate of petal lobe growth, even in a plena mutant background. This implies that fistulata normally has two roles in the distal domain of petal primordia: inhibition of plena expression and promotion of lobe growth. A weak allele of the floral meristem identity gene, floricaula, greatly enhances the effect of fistulata on plena expression, showing that floricaula also plays a role in repression of plena in outer whorls. Taken together, these results show that genes involved in plena regulation have additional roles in the formation of organs, perhaps reflecting underlying mechanisms for coupling homeotic gene expression to morphogenesis.

Transcription pattern of a FIM homologue in Impatiens during floral development and reversion.

Flowering and reversion in Impatiens are characterised by gradual transitions of organ identity and constitute a unique system for the molecular and physiological study of floral organogenesis. The authors have isolated an Impatiens homologue of the FIM gene of Antirrhinum (UFO in Arabidopsis), Imp-FIM, and analysed its expression in three states of the terminal meristem: vegetative, floral, and reverted. In floral meristems, Imp-FIM transcription is associated with petal identity, as in Antirrhinum and Arabidopsis, but this is achieved through a novel transcription pattern, characterised by a high level of transcript within petal primordia. This novel transcription pattern could contribute to the more diffuse boundaries between organ types in Impatiens. In vegetative meristems, Imp-FIM is expressed in the axils of leaf primordia which are arranged in a spiral. A similar pattern is observed in reverted meristems in which leaf primordia are initiated in a whorled arrangement. This result indicates that the maintenance of floral phyllotaxis is not associated with a specific pattern of Imp-FIM transcription. Transcription of Imp-FIM in a non-reverting line is no different from that in the reverting line. Therefore, the lack of floral commitment in the reverting line does not seem to be responsible for Imp-FIM transcription within petals. The novel transcription pattern in petals, together with features of Impatiens that are reminiscent of fim and ufo mutant phenotypes suggest an evolutionary divergence for Imp-FIM regulation in this species.