CIPK-B is essential for salt stress signalling in Marchantia polymorpha.

Calcium signalling is central to many plant processes, with families of calcium decoder proteins having expanded across the green lineage and redundancy existing between decoders. The liverwort Marchantia polymorpha has fast become a new model plant, but the calcium decoders that exist in this species remain unclear. We performed phylogenetic analyses to identify the calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) network of M. polymorpha. We analysed CBL-CIPK expression during salt stress, and determined protein-protein interactions using yeast two-hybrid and bimolecular fluorescence complementation. We also created genetic knockouts using CRISPR/Cas9. We confirm that M. polymorpha has two CIPKs and three CBLs. Both CIPKs and one CBL show pronounced salt-responsive transcriptional changes. All M. polymorpha CBL-CIPKs interact with each other in planta. Knocking out CIPK-B causes increased sensitivity to salt, suggesting that this CIPK is involved in salt signalling. We have identified CBL-CIPKs that form part of a salt tolerance pathway in M. polymorpha. Phylogeny and interaction studies imply that these CBL-CIPKs form an evolutionarily conserved salt overly sensitive pathway. Hence, salt responses may be some of the early functions of CBL-CIPK networks and increased abiotic stress tolerance required for land plant emergence.

Microbial communities in the tropical air ecosystem follow a precise diel cycle.

The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.

Empirica: a virtual lab for high-throughput macro-level experiments.

Virtual labs allow researchers to design high-throughput and macro-level experiments that are not feasible in traditional in-person physical lab settings. Despite the increasing popularity of online research, researchers still face many technical and logistical barriers when designing and deploying virtual lab experiments. While several platforms exist to facilitate the development of virtual lab experiments, they typically present researchers with a stark trade-off between usability and functionality. We introduce Empirica: a modular virtual lab that offers a solution to the usability-functionality trade-off by employing a "flexible defaults" design strategy. This strategy enables us to maintain complete "build anything" flexibility while offering a development platform that is accessible to novice programmers. Empirica's architecture is designed to allow for parameterizable experimental designs, reusable protocols, and rapid development. These features will increase the accessibility of virtual lab experiments, remove barriers to innovation in experiment design, and enable rapid progress in the understanding of human behavior.

Fostering responsible research with genome editing technologies: a European perspective.

In this consensus paper resulting from a meeting that involved representatives from more than 20 European partners, we recommend the foundation of an expert group (European Steering Committee) to assess the potential benefits and draw-backs of genome editing (off-targets, mosaicisms, etc.), and to design risk matrices and scenarios for a responsible use of this promising technology. In addition, this European steering committee will contribute in promoting an open debate on societal aspects prior to a translation into national and international legislation.

Recovery-oriented care in acute inpatient mental health settings: an exploratory study.

Australian mental health nurses will need to care with consumers of mental health services, within the domains of recovery. However, in acute inpatient mental health settings, nurses are without a clear description of how to be recovery-oriented. The intent of this qualitative study was to ask nurses to reflect on and describe current practice within acute inpatient services that are not overtly recovery-oriented. Results show that nurses can identify recovery and articulate with pragmatic clarity how to care within a recovery-oriented paradigm. Pragmatic modes of care described by nurses support using "champions" to assist with eventual system transformation in the delivery of mental health services.

A Review of Particle Size Analysis with X-ray CT.

Particle size and morphology analysis is a problem common to a wide range of applications, including additive manufacturing, geological and agricultural materials' characterisation, food manufacturing and pharmaceuticals. Here, we review the use of microfocus X-ray computed tomography (X-ray CT) for particle analysis. We give an overview of different sample preparation methods, image processing protocols, the morphology parameters that can be determined, and types of materials that are suitable for analysis of particle sizes using X-ray CT. The main conclusion is that size and shape parameters can be determined for particles larger than approximately 2 to 3 µm, given adequate resolution of the X-ray CT setup. Particles composed of high atomic number materials (Z > 40) require careful sample preparation to ensure X-ray transmission. Problems occur when particles with a broad range of sizes are closely packed together, or when particles are fused (sintered or cemented). The use of X-ray CT for particle size analysis promises to become increasingly widespread, offering measurements of size, shape, and porosity of large numbers of particles within one X-ray CT scan.

The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters.

Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their identity and ecology is not well established. Cellulose is a major component of landfill waste and its degradation is therefore a key feature of the anaerobic microbial decomposition process. Here, we targeted a number of taxa containing known cellulolytic anaerobes (members of the bacterial genus Fibrobacter, lineages of Clostridium clusters I, III, IV and XIV, and anaerobic fungi of the Neocallimastigales) in landfill leachate and colonized cellulose 'baits' via PCR and quantitative PCR (qPCR). Fibrobacter spp. and Clostridium clusters III, IV and XIV were detected in almost all leachate samples and cluster III and XIV clostridia were the most abundant (1-6% and 1-17% of total bacterial 16S rRNA gene copies respectively). Two landfill leachate microcosms were constructed to specifically assess those microbial communities that colonize and degrade cellulose substrates in situ. Scanning electron microscopy (SEM) of colonized cotton revealed extensive cellulose degradation in one microcosm, and Fibrobacter spp. and Clostridium cluster III represented 29% and 17%, respectively, of total bacterial 16S rRNA gene copies in the biofilm. Visible cellulose degradation was not observed in the second microcosm, and this correlated with negligible relative abundances of Clostridium cluster III and Fibrobacter spp. (≤ 0.1%), providing the first evidence that the novel fibrobacters recently detected in landfill sites and other non-gut environments colonize and degrade cellulose substrates in situ.

Action learning sets for supporting postgraduate mental health nurses' transition to professional practice: A qualitative study.

This paper reports on a qualitative case study of postgraduate mental health nurses participating in a monthly facilitated action learning set (ALS) in order to support them while they transition from PGMHN to independent professional practice. The aim of the study was to determine what the impact of participating in an ALS would have on how they perceived clinical practice issues. The ALS comprised a small group of PGMHN supported by a facilitator in order to explore issues from clinical practice by using Socratic questions to challenge their thinking. Data were collected via a single focus group and a 20-item survey. Focus group textual data were coded line by line, and codes were synthesized thematically. The major theme to emerge from the qualitative results was as follows: 'Learning from doing an action learning set'. Three subthemes were identified: Think outside the box: Developing Socratic questions; there's rarely one right way: Applying action learning to practice; and Not easy to implement: Action plans in action. A 20-item evaluative survey indicated that ALS increased participant's confidence as a mental health nurse. Using critical questions increased participants' confidence to explore different perspectives when engaged in problem-solving.

Assessment of Factors Impacting Long-Term Utilization of Tracheoesophageal Speech Among Laryngectomees.

OBJECTIVE(S): To evaluate complication rate and abandonment rate after tracheoesophageal puncture and to assess factors associated with these outcome measures. METHODS: Retrospective review of laryngectomy patients seen at a single academic institution between 1/1/2003 and 12/1/2018. Charts reviewed for demographics, medical comorbidities, tumor characteristics, surgical data, adjuvant treatment history, and complications related to laryngectomy or tracheoesophageal puncture. Complications were divided into minor and major. RESULTS: A total of 293 laryngectomees met inclusion criteria. Of these, 69 patients (23.5%) underwent tracheoesophageal puncture. Average follow up was 64.6 months (SD 58.3). Overall laryngectomy complication rate was 43.3%. Overall tracheoesophageal puncture complication rate was 73.9%, with 39.1% of patients having major complications and 34.8% having minor complications only. Total abandonment rate for tracheoesophageal puncture was 34.8%. No associations were seen between tracheoesophageal puncture complication or abandonment rates based on age, gender, race, or insurance status. An increased rate of laryngectomy complications was seen after primary tracheoesophageal puncture (76.5% vs 41.3%, P = .005). CONCLUSION: Tracheoesophageal puncture outcomes were similar in patients with varied demographic, medical, and treatment backgrounds. When considering timing, our findings suggest that patients should be counseled on the possibility of increased complication risk after primary tracheoesophageal puncture. In those in whom the surgeon already has concerns about wound healing, it may be prudent to avoid primary tracheoesophageal puncture. The relatively high abandonment rate emphasizes the value of this measure of tracheoesophageal puncture outcome and highlights the need for appropriate patient counseling and prospective studies assessing the decision to abandon.

Is thoracoscopic esophageal atresia repair safe in the presence of cardiac anomalies?

BACKGROUND: Esophageal atresia (EA) is often associated with congenital heart disease (CHD). Repair of EA by the thoracoscopic approach places physiological stress on a newborn with CHD. This paper reviews the outcomes of infants with CHD who had undergone thoracoscopic EA repair, comparing their outcomes to those without CHD. METHODS: This was a review of infants who underwent thoracoscopic EA repair from 2009 to 2017 at one institution. Operative time and outcomes were analyzed in relation to CHD status. RESULTS: Twenty five infants underwent thoracoscopic EA repair during the study period. Seventeen (68%) had associated anomalies of whom 9 (36%) had cardiac anomalies. The mean operative time was 217 min. There was no difference in operative time between CHD and non-CHD cases (estimate 20 min longer operative time in the presence of a cardiac anomaly [95% CI -20 to 57]). Two cases were converted to open thoracotomy; both were non-CHD. There was no difference in the time to feeding, time in intensive care unit or time in hospital between CHD and non-CHD cases. Five patients developed an anastomotic leak (two CHD and three non-CHD) of which two were clinical; all were managed conservatively. There was no case of recurrent fistula. CONCLUSIONS: This pilot study did not find evidence that thoracoscopic EA repair compromised outcomes in children with congenital heart disease. A prospective multicenter study with long-term follow-up is recommended to confirm whether thoracoscopic repair in CHD is truly equivalent to the open operation. TYPE OF STUDY: Therapeutic. LEVEL OF EVIDENCE: Level III.

Complete genome of Enterobacter sichuanensis strain SGAir0282 isolated from air in Singapore.

BACKGROUND: Enterobacter cloacae complex (ECC) bacteria, such as E. cloacae, E. sichuanensis, E. kobei, and E. roggenkampii, have been emerging as nosocomial pathogens. Many strains isolated from medical clinics were found to be resistant to antibiotics, and in the worst cases, acquired multidrug resistance. We present the whole genome sequence of SGAir0282, isolated from the outdoor air in Singapore, and its relevance to other ECC bacteria by in silico genomic analysis. RESULTS: Complete genome assembly of E. sichuanensis strain SGAir0282 was generated using PacBio RSII and Illumina MiSeq platforms, and the datasets were used for de novo assembly using Hierarchical Genome Assembly Process (HGAP) and error corrected with Pilon. The genome assembly consisted of a single contig of 4.71 Mb and with a G+C content of 55.5%. No plasmid was detected in the assembly. The genome contained 4371 coding genes, 83 tRNA and 25 rRNA genes, as predicted by NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Among the genes, the antibiotic resistance related genes were included: Streptothricin acetdyltransferase (SatA), fosfomycin resistance protein (FosA) and metal-dependent hydrolases of the beta-lactamase superfamily I (BLI). CONCLUSION: Based on whole genome alignment and phylogenetic analysis, the strain SGAir0282 was identified to be Enterobacter sichuanensis. The strain possesses gene clusters for virulence, disease and defence, that can also be found in other multidrug resistant ECC type strains.

Whole-Genome Sequence of Bacillus megaterium Strain SGAir0080, Isolated from an Indoor Air Sample.

Bacillus megaterium strain SGAir0080 was isolated from a tropical air sample in Singapore. Its genome was assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads. It has one chromosome of 5.06 Mbp and seven plasmids (average length, 62.8 kbp). It possesses 5,339 protein-coding genes, 130 tRNAs, and 35 rRNAs.

Complete Genome Sequence of Lysinibacillus sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore.

Lysinibacillus sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.

Complete Genome Sequence of Nissabacter sp. Strain SGAir0207, Isolated from an Air Sample Collected in Singapore.

Nissabacter sp. strain SGAir0207 was isolated from a tropical air sample collected in Singapore. Its genome was assembled using a hybrid approach with long and short reads, resulting in one chromosome of 3.9 Mb and 7 plasmids. The complete genome consists of 4,403 protein-coding, 84 tRNA, and 22 rRNA genes.

Complete Genome Sequence of Brachybacterium sp. Strain SGAir0954, Isolated from Singapore Air.

Brachybacterium sp. strain SGAir0954 was isolated from tropical air collected in Singapore, and its genome was sequenced and assembled using long reads generated by single-molecule real-time (SMRT) sequencing. The complete genome has a size of 3.41 Mb and consists of 2,955 protein coding genes, 50 tRNAs, and 9 rRNAs.

Complete Genome Sequence of Agrococcus sp. Strain SGAir0287, Isolated from Tropical Air Collected in Singapore.

Agrococcus sp. strain SGAir0287 was isolated from tropical air samples collected in Singapore. Assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads, the genome consists of one circular chromosome of 3,084,767 bp. The entire genome has 2,870 protein-coding genes, 45 tRNAs, and 3 rRNAs.

Genome Sequence of the Tropical Atmosphere Bacterium Pontibacter sp. Strain SGAir0037.

The Pontibacter bacterial genus has been detected in marine and soil environments. Here, we report the genome sequence of Pontibacter sp. strain SGAir0037, which was isolated from outdoor air samples collected in Singapore. The genome comprises one chromosome of 5.26 Mb and one plasmid of 127 kb.

Complete Genome Sequence of Microbacterium sp. Strain SGAir0570, Isolated from Tropical Air Collected in Singapore.

Microbacterium sp. strain SGAir0570 was isolated from air samples collected in Singapore. Its genome was assembled using single-molecule real-time sequencing and MiSeq short reads. It has one chromosome with a length of 3.38 Mb and one 59.2-kb plasmid. It contains 3,170 protein-coding genes, 48 tRNAs, and 6 rRNAs.

Complete Genome Sequence of Pseudomonas sp. Strain SGAir0191, Isolated from Tropical Air Collected in Singapore.

Pseudomonas sp. strain SGAir0191 was isolated from an air sample collected in Singapore, and its genome was sequenced using a combination of long and short reads to generate a high-quality genome assembly. The complete genome is approximately 5.07 Mb with 4,370 protein-coding genes, 19 rRNAs, and 73 tRNAs.

Complete Genome Sequence of the Bacterium Serratia marcescens SGAir0764, Isolated from Singapore Air.

Serratia marcescens strain SGAir0764 was isolated from a tropical air sample collected in Singapore. The complete genome, sequenced on the PacBio RS II platform, consists of one chromosome with 5.1 Mb and one plasmid with 76.4 kb. Genome annotation predicts 4,723 protein-coding genes, 89 tRNAs, and 22 rRNAs.