Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis

The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.

Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases

BACKGROUND

Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown.

METHODS

In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform.

RESULTS

Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level.

CONCLUSIONS

Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.

Maximum Likelihood Reconstruction of Water Cherenkov Events With Deep Generative Neural Networks

Large water Cherenkov detectors have shaped our current knowledge of neutrino physics and nucleon decay, and will continue to do so in the foreseeable future. These highly capable detectors allow for directional and topological, as well as calorimetric information to be extracted from signals on their photosensors. The current state-of-the-art approach to water Cherenkov reconstruction relies on maximum-likelihood estimation, with several simplifying assumptions employed to make the problem tractable. In this paper, we describe neural networks that produce probability density functions for the signals at each photosensor, given a set of inputs that characterizes a particle in the detector. The neural networks we propose allow for likelihood-based approaches to event reconstruction with significantly fewer assumptions compared to traditional methods, and are thus expected to improve on the current performance of water Cherenkov detectors.

Short-range contributions of local sources to ambient air

Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m² tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.

First Asian validation of ORBI score in predicting in-hospital cardiogenic shock in patients with ST-segment elevation myocardial infarction treated by primary percutaneous coronary intervention

Background

Cardiogenic shock (CS) complicating an acute coronary syndrome still worsening the prognosis with 30-day mortality rates approximating 40–45%, despite improvements in the acute management of ST-segment elevation myocardial infarction (STEMI), particularly the widespread use of timely primary percutaneous coronary intervention (pPCI). The ORBI risk score provides a readily useable and efficient tool to identify patients at high-risk of developing CS during hospitalization following STEMI which may aid in further risk-stratification and thus potentially facilitate pre-emptive clinical decision making. This is essential in developing countries with wide variation in health care facilities, scarce resources and increasing burden of cardiovascular diseases.

Purpose

To validate ORBI Score in identifying patients at high-risk of in-hospital STEMI related cardiogenic shock in a multi-ethnic developing country.

Method

The ORBI risk score was evaluated in 1934 patients STEMI without CS on admission and treated by primary percutaneous coronary intervention (pPCI) in our national cardiovascular centre included this study. Model discrimination and calibration was tested in the overall population. Eleven variables from the ORBI score were independently associated with the development of in-hospital CS: age >70 years, prior stroke/transient ischaemic attack, cardiac arrest upon admission, anterior STEMI, first medical contact-to-pPCI delay >90min, Killip class, heart rate >90/min, a combination of systolic blood pressure <125 mmHg and pulse pressure <45 mmHg, glycaemia >10 mmol/L, culprit lesion of the left main coronary artery, and post-pPCI thrombolysis in myocardial infarction flow grade <3. The score derived from these variables allowed the classification of patients into four risk categories: low (0–7), low- to-intermediate (8–10), intermediate-to-high (11–12), and high (≥13).

Results

Observed in-hospital CS rates were 0.3%, 6.4%, 19.5%, and 32.12%, across the four risk categories, respectively. The score demonstrated high discrimination (c-statistic of 0.91 (CI 95% 0.88–0.93), p<0.001 in the validation cohort)

Conclusion

The ORBI risk score is valid and can be used for predicting the development of cardiogenic shock in STEMI patients for better targeted treatment.

Funding Acknowledgement

Type of funding sources: None. ROC curveObserved in-hospital CS rates

The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air

Background

Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. The ability to produce endospores and biofilms contribute to their pathogenicity, classified in two types of food poisoning: diarrheal and emetic syndromes. Here we report gap-free, whole-genome sequences of two B. cereus strains isolated from air samples and analyse their emetic and diarrheal potential.

Results

Genome assemblies of the B. cereus strains consist of one chromosome and seven plasmids each. The genome size of strain SGAir0260 is 6.30-Mb with 6590 predicted coding sequences (CDS) and strain SGAir0263 is 6.47-Mb with 6811 predicted CDS. Macrosynteny analysis showed 99% collinearity between the strains isolated from air and 90.2% with the reference genome. Comparative genomics with 57 complete B. cereus genomes suggests these strains from air are closely associated with strains isolated from foodborne illnesses outbreaks. Due to virulence potential of B. cereus and its reported involvement in nosocomial infections, antibiotic resistance analyses were performed and confirmed resistance to ampicillin and fosfomycin, with susceptibility to ciprofloxacin, tetracycline and vancomycin in both strains.

Conclusion

Phylogenetic analysis combined with detection of haemolytic (hblA, hblC, and hblD) and non-haemolytic (nheA, nheB, and nheC) enterotoxin genes in both air-isolated strains point to the diarrheic potential of the air isolates, though not emetic. Characterization of these airborne strains and investigation of their potential disease-causing genes could facilitate identification of environmental sources of contamination leading to foodborne illnesses and nosocomial infections transported by air.

Complete Genome Sequence of Penicillium oxalicum Strain SGAir0226 Isolated from Outdoor Tropical Air in Singapore

Penicillium oxalicum strain SGAir0226 was isolated from a tropical air sample collected in Singapore. The complete genome was assembled from long reads obtained from single-molecule real-time sequencing and was further polished and error corrected using short read sequencing data. The assembly comprises 20 contigs with a total length of 30.7 Mb. The genome was predicted to contain 8310 protein-coding genes, 237 tRNAs and 83 rRNAs.

Whole-Genome Sequencing of Aspergillus terreus Species Complex

Aspergillus terreus species complex is an opportunistic fungal pathogen increasingly implicated in invasive infection, as well as chronic respiratory disease. Currently, an understanding of A. terreus pathogenicity is impeded by a limited number of whole-genome sequences of this fungal pathogen. We here describe a high-quality whole-genome assembly of European A. terreus clinical isolate M6925, derived by single-molecule real-time sequencing with short-read polishing.

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.

Magnetic phases of spin-1 spin-orbit-coupled Bose gases

Phases of matter are characterized by order parameters describing the type and degree of order in a system. Here we experimentally explore the magnetic phases present in a near-zero temperature spin-1 spin-orbit-coupled atomic Bose gas and the quantum phase transitions between these phases. We observe ferromagnetic and unpolarized phases, which are stabilized by spin-orbit coupling's explicit locking between spin and motion. These phases are separated by a critical curve containing both first- and second-order transitions joined at a tricritical point. The first-order transition, with observed width as small as h × 4 Hz, gives rise to long-lived metastable states. These measurements are all in agreement with theory.

Antifouling activity of synthetic polymer gels against cyprids of the barnacle (Balanus amphitrite) in vitro

Barnacle (Balanus amphitrite) settlement on synthetic hydrogels with various chemical structures was tested in laboratory assays. The results demonstrated that cyprids settle less or not at all on hydrogels and PDMS elastomer compared with the polystyrene control. The low settlement on gels is most likely due to the 'easy release' of initially attached cyprids from the gel surfaces. This low adhesion of cyprids is independent of surface hydrophilicity or hydrophobicity, and of surface charge. The results also revealed that hydrogels can be categorized into two groups. One group showed an extremely strong antifouling (AF) performance that was independent of the elasticity (E) or swelling degree (q) of the gels. The second group showed relatively less strong AF performance that was E- or q-dependent. In the latter case, E, rather than the q, may be the more important factor for cyprid settlement.