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Habitat selection is the process by which an individual makes an active decision to make use of a particular habitat when others are available. The ability to infer habitat selection therefore requires observations of movement through space and time which can be particularly challenging for marine species that are cryptic and do not regularly visit the sea surface. Rajidae (skates) are benthic mesopredators that inhabit turbid coastal waters and exhibit site fidelity, making them an ideal group for studying habitat selection and resource partitioning using a fixed, passive acoustic receiver array in the western English Channel, UK. Using network analysis, significant differences were found in the way 4 species of Rajidae occupied different parts of the array; for example, Raja microocellata and R. clavata occupied shallower habitat than R. brachyura and R. montagui. R. montagui and R. brachyura were further separated, with each species detected more frequently at different receivers. Males and females of all 4 species were also detected at different receivers and at different times. These results demonstrate habitat selection, resource partitioning among species and sexual segregation in these 4 species of Rajidae. Our findings are important evidence for management of fisheries, such as the designation of marine protected areas, and further highlight the potential of this method for tracking other mobile marine species in temperate, open coastal regions.

Here, we describe taxonomical composition, as well as seasonal and diel dynamics of airborne microbial communities in West Siberia. A total of 78 airborne biomass samples from 39 time intervals were analysed, within a temperature range of 48 °C (26 °C to - 22 °C). We observed a 5-170-fold decrease in DNA yield extracted from the airborne biomass in winter compared to summer, nevertheless, yielding sufficient material for metagenomic analysis. The airborne microbial communities included Actinobacteria and Proteobacteria, Ascomycota and Basidiomycota fungi as major components, as well as some Streptophyta plants. In summer, bacterial and fungal plant pathogens, and wood-rotting saprophytes were predominant. In winter, Ascomycota moulds and cold-related or stress environment bacterial species were enriched, while the fraction of wood-rotting and mushroom-forming Basidiomycota fungi was largely reduced. As recently reported for the tropical climate, the airborne microbial communities performed a diel cycle in summer, however, in winter diel dynamics were not observed. Ministry of Education (MOE) Published version This study was supported by Academic Research Fund (AcRF) Tier 3, Singapore Ministry of Education (grant number: MOE2013-T3-1-013). V.N.K and V.A.S were supported by the Russian Foundation of Basic Research (Project #18-29-13045). We thank Dr. Sharon Longford, Senior Assistant Director, Science Communications, Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University for critical reading of this manuscript.

Tetanus is a fatal disease caused by Clostridium tetani infections. To prevent infections, a toxoid vaccine, developed almost a century ago, is routinely used in humans and animals. The vaccine is listed in the World Health Organisation list of Essential Medicines and can be produced and administered very cheaply in the developing world for less than one US Dollar per dose. Recent developments in both analytical tools and frameworks for systems biology provide industry with an opportunity to gain a deeper understanding of the parameters that determine C. tetani virulence and physiological behaviour in bioreactors. Here, we compared a traditional fermentation process with a fermentation medium supplemented with five heavily consumed amino acids. The experiment demonstrated that amino acid catabolism plays a key role in the virulence of C. tetani. The addition of the five amino acids favoured growth, decreased toxin production and changed C. tetani morphology. Using time-course transcriptomics, we created a “fermentation map”, which shows that the tetanus toxin transcriptional regulator BotR, P21 and the tetanus toxin gene was downregulated. Moreover, this in-depth analysis revealed potential genes that might be involved in C. tetani virulence regulation. We observed differential expression of genes related to cell separation, surface/cell adhesion, pyrimidine biosynthesis and salvage, flagellar motility, and prophage genes. Overall, the fermentation map shows that, mediated by free amino acid concentrations, virulence in C. tetani is regulated at the transcriptional level and affects a plethora of metabolic functions.

Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.

While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.

Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed.

Coexistence of ecologically similar species occupying the same geographic location (sympatry) poses questions regarding how their populations persist without leading to competitive exclusion. There is increasing evidence to show that micro-variations in habitat use may promote coexistence through minimising direct competition for space and resources. We used two sympatric marine predators that show high fidelity to a small, remote coral atoll as a model to investigate how temporally dynamic partitioning of space use may promote coexistence. Using novel methods (difference network analysis and dynamic space occupancy analysis), we revealed that even though blacktip reef sharks Carcharhinus melanopterus and sicklefin lemon sharks Negaprion acutidens both show focused use of the same atoll habitats, the spatio-temporal dynamics of their use was partitioned such that they only shared the same microhabitats 26% of the time. Moreover, the degree of overlap was strongly influenced by the tidal cycle, peaking at ~35% at higher tides as both species appear to target similar intertidal micro-habitats despite the increase in available space. Our work provides a rare example of how two marine predators with similar ecological roles and habitat preferences may coexist in the same place through dynamic segregation of habitat use in space and time, potentially reflecting adaptive behavioural traits for minimising interactions. The strong influence of small tidal variation on species habitat use and partitioning also raises concerns over how atoll ecosystem dynamics may be influenced by sea level rises that could alter tidal dynamics.

Chytrids are early-diverging fungi that share features with animals that have been lost in most other fungi. They hold promise as a system to study fungal and animal evolution, but we lack genetic tools for hypothesis testing. Here, we generated transgenic lines of the chytrid Spizellomyces punctatus, and used fluorescence microscopy to explore chytrid cell biology and development during its life cycle. We show that the chytrid undergoes multiple rounds of synchronous nuclear division, followed by cellularization, to create and release many daughter ‘zoospores’. The zoospores, akin to animal cells, crawl using actin-mediated cell migration. After forming a cell wall, polymerized actin reorganizes into fungal-like cortical patches and cables that extend into hyphal-like structures. Actin perinuclear shells form each cell cycle and polygonal territories emerge during cellularization. This work makes Spizellomyces a genetically tractable model for comparative cell biology and understanding the evolution of fungi and early eukaryotes.

Exogenous glycine betaine (GB) or hydrogen peroxide (H2O2) application has not been explored to mitigate waterlogging stress in Andean fruit trees. The objective of this study was to evaluate foliar GB or H2O2 application on the physiological behavior of Cape gooseberry plants under waterlogging. Two separate experiments were carried out. In the first trial, the treatment groups were: (1) plants without waterlogging and with no foliar applications, (2) plants with waterlogging and without foliar applications, and (3) waterlogged plants with 25, 50, or 100 mM of H2O2 or GB, respectively. The treatments in the second trial were: (1) plants without waterlogging and with no foliar applications, (2) plants with waterlogging and without foliar applications, and (3) waterlogged plants with 100 mM of H2O2 or GB, respectively. In the first experiment, plants with waterlogging and with exogenous GB or H2O2 applications at a dose of 100 mM showed higher leaf water potential (&minus, 0.5 Mpa), dry weight (1.0 g), and stomatal conductance (95 mmol&middot, m&minus, 2&middot, s&minus, 1) values. In the second experiment, exogenously supplied GB or H2O2 also increased the relative growth rate, and leaf photosynthesis mitigating waterlogging stress. These results show that short-term GB or H2O2 supply can be a tool in managing waterlogging in Cape gooseberry.

Background The origin of the intercalated cushions that develop into the anterior cusp of the pulmonary valve (PV) and the noncoronary cusp of the aortic valve (AV) is not well understood. Results Cre transgenes in combination with the Rosa TdTomato-EGFP reporter were used to generate three-dimensional lineage mapping of AV and PV cusps during intercalated cushion development. Tie2-Cre;EGFP was used to mark endothelial-derived mesenchymal cells, Wnt1-Cre;EGFP for cardiac neural crest and cardiac Troponin T (Tnnt2)Cre;EGFP, for myocardial lineage. The highest percentage of intercalated cushion cells at embryonic day (E) 12.5 was Tnnt2-Cre; EGFP positive; 68.0% for the PV and 50.0% AV. Neither Tnnt2 mRNA nor Tnnt2-Cre protein was expressed in the intercalated cushions; and the Tnnt2-Cre lineage intercalated cushion cells were also positive for the mesenchymal markers Sox9 and versican. Tnnt2-Cre lineage was present within the forming intercalated cushions from E11.5 and was present in the intercalated cushion derived PV and AV cusps and localized to the fibrosa layer at postnatal day 0. Conclusions Intercalated cushions of the developing outflow tract are populated with Tnnt2-Cre derived cells, a Cre reporter previously used for tracing and excision of myocardial cells and not previously associated with mesenchymal cells. Developmental Dynamics 247:1005-1017, 2018. © 2018 Wiley Periodicals, Inc.

Additional co-authors: G. Peirson, K. K. Richter, M. I. Taylor,C. N. Trueman, B. Hayden, J. R. Stevens

Management and conservation of marine predator species relies on a fundamental knowledge of their movements and behaviour. Pop‐up satellite archival tags were used to investigate the vertical movement patterns of five blue sharks (Prionace glauca) and one thresher shark (Alopias vulpinus) within the southeastern Indian Ocean. Sections of similar depth distribution, identified using a split moving window analysis, were investigated in relation to the thermal structure of the water column and activity rates. Minimum horizontal displacement of between 66 and 5,187 km for blue sharks and 16 km for the thresher shark were recorded over 863 tracking days. Maximum depths ranged from 540 to 807 m for blue sharks and 144 m for the thresher shark. All sharks displayed plasticity in their depth distribution, with diel vertical movements and surface‐oriented movements the two most common patterns. Diel movement of prey is the most likely explanation for diel vertical movements of thresher and blue sharks. This study has improved our understanding of the vertical movement patterns of these pelagic predators and the relationship between their depth distribution, temperature, and activity.

The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD-CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein-E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.

Background: The prevalence of youth athletes specializing in 1 sport has been increasing over the past decade. Subsequently, the rate of youth athlete injury has also been increasing. It is possible that an association exists between youth specialization and sports injury rate. Purpose: To determine if sport sampling is associated with a lower sports injury rate in youths compared with youths who specialize in 1 sport. Study Design: Systematic review and meta-analysis. Methods: A systematic review was conducted following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines using PubMed, Embase, and the Cochrane library. Inclusion criteria included studies written in the English language, studies with athletes between 7 and 18 years of age, studies that report injury rates, and studies that specify if athletes were sport samplers or specialized in a sport. Data relevant to this study, including injuries and patient characteristics, were extracted and statistically analyzed. Results: The initial search identified 324 studies, 6 of which met inclusion criteria. From these 6 studies, the total participant number was 5736. Of those, 2451 (42.7%) were “sport samplers,” 1628 (28.4%) were “sport specializers,” and 1657 (28.9%) were considered “others” (ie, could not be classified as true samplers or true specializers). The average age of all the athletes was 14.6 years (range, 7-18 years). Sport specializers had a significantly higher injury risk than the sport samplers (RR, 1.37; 95% CI, 1.19-1.57; P < .0001). There was a higher risk of injury in the “others” group when compared with the “sport sampler” group (RR, 1.21; 95% CI, 1.14-1.29; P < .0001). There was a higher risk of injury in the “sport specializer” group over the “others” group (RR, 1.09; 95% CI, 1.04-1.14; P < .005). Conclusion: Sport sampling is associated with a decreased risk of sports injury in youth athletes when compared with those who specialize in 1 sport. Injury rates increase as a youth athlete becomes increasingly specialized. Youth athletes would benefit substantially from participating in sport sampling.

Background and purpose There are no medications currently available to treat metabolic inflammation. Bruton's tyrosine kinase (BTK) is highly expressed in monocytes and macrophages and regulates NF-κB and NLRP3 inflammasome activity; both propagate metabolic inflammation in diet-induced obesity. Experimental approach Using an in vivo model of chronic inflammation, high-fat diet (HFD) feeding, in male C57BL/6J mice and in vitro assays in primary murine and human macrophages, we investigated if ibrutinib, an FDA approved BTK inhibitor, may represent a novel anti-inflammatory medication to treat metabolic inflammation. Key results HFD-feeding was associated with increased BTK expression and activation, which was significantly correlated with monocyte/macrophage accumulation in the liver, adipose tissue, and kidney. Ibrutinib treatment to HFD-fed mice inhibited the activation of BTK and reduced monocyte/macrophage recruitment to the liver, adipose tissue, and kidney. Ibrutinib treatment to HFD-fed mice decreased the activation of NF-κB and the NLRP3 inflammasome. As a result, ibrutinib treated mice fed HFD had improved glycaemic control through restored signalling by the IRS-1/Akt/GSK-3β pathway, protecting mice against the development of hepatosteatosis and proteinuria. We show that BTK regulates NF-κB and the NLRP3 inflammasome specifically in primary murine and human macrophages, the in vivo cellular target of ibrutinib. Conclusion and implications We provide "proof of concept" evidence that BTK is a novel therapeutic target for the treatment of diet-induced metabolic inflammation and ibrutinib may be a candidate for drug repurposing as an anti-inflammatory agent for the treatment of metabolic inflammation in T2D and microvascular disease.

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.

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.

Chytrids are early-diverging fungi that share ancestral features of animals, including cells that crawl and swim. At later stages, chytrid cells resemble fungi with a chitin-based cell wall and hyphal-like structures known as rhizoids. Chytrids are important evolutionary transitional forms, but much remains unknown about their cell biology because we lack genetic tools for the live-cell imaging of their nuclear and cytoskeletal dynamics. Here, we generated stable transgenic lines of the soil chytrid Spizellomyces punctatus, and coupled live-cell microscopy and fluorescent tagging to measure the timing and coordination of growth, the cell cycle, and the actin cytoskeleton. We show that Spizellomyces zoospores rapidly encyst, develop rhizoids, and undergo multiple rounds of synchronous nuclear division in a sporangium, followed by cellularization, to create and release hundreds of zoospores. The life cycle is complete in less than 30 hours. We further demonstrate that crawling zoospores, akin to animal cells, display polymerized actin at the leading edge of amoeboid fronts. After encystment, polymerized actin reorganizes into fungal-like cortical patches and cables that extend into the rhizoid. Actin remains highly dynamic during sporo-genesis with the formation of actin perinuclear shells each cell cycle and the emergence of polygonal territories during cellularization. Spizellomyces is a fast-growing and genetically-tractable organism that should be useful for comparative cell biology and understanding the evolution of fungi and early eukaryotes.

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.

Clostridium is a broad genus of anaerobic, spore-forming, rod-shaped, Gram-positive bacteria that can be found in different environments all around the world. The genus includes human and animal pathogens that produce potent exotoxins that cause rapid and potentially fatal diseases responsible for countless human casualties and billion-dollar annual loss to the agricultural sector. Diseases include botulism, tetanus, enterotoxemia, gas gangrene, necrotic enteritis, pseudomembranous colitis, blackleg, and black disease, which are caused by pathogenic Clostridium. Due to their ability to sporulate, they cannot be eradicated from the environment. As such, immunization with toxoid or bacterin-toxoid vaccines is the only protective method against infection. Toxins recovered from Clostridium cultures are inactivated to form toxoids, which are then formulated into multivalent vaccines. This review discusses the toxins, diseases, and toxoid production processes of the most common pathogenic Clostridium species, including Clostridium botulinum, Clostridium tetani, Clostridium perfringens, Clostridium chauvoei, Clostridium septicum, Clostridium novyi and Clostridium hemolyticum.

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.

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.

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.

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.

Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.

The associated article was published under the title Genome Announcements (ISSN: 2169-8287). In July 2018, Genome Announcements was renamed Microbiology Resource Announcements. Volume 6, no. 22, e00424-18, 2018, [https://doi.org/10.1128/genomeA.00424-18][1]. Page 1: The title should appear as given

Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81 tRNAs, and 24 rRNAs.

The associated article was published under the title Genome Announcements (ISSN: 2169-8287). In July 2018, Genome Announcements was renamed Microbiology Resource Announcements. Volume 6, no. 19, e00229-18, 2018, [https://doi.org/10.1128/genomeA.00229-18][1]. Page 1: The title should appear as given

A sympatric assemblage of morphologically similar predators is expected to exhibit fine-scale habitat segregation, or resource partitioning, to reduce the effects of direct competition. This principle has been well studied for predators in terrestrial ecosystems. In the marine environment, the fine-scale spatial segregation of sympatric species of large predators is poorly understood because detailed movement and behavioural data are often not available across multiple species within the same timeframe. The ways in which co-occurring congeneric predators separate spatially is even less well understood. Medium-sized species of skates (genus Raja) co-occur in temperate habitats of the north-east Atlantic Ocean, share similar morphologies and have distributional ranges that overlap significantly in the western English Channel ecosystem. In the present study, detailed depth time series retrieved from 89 electronic data storage tags attached to 4 species of skate were analysed to determine preferred depth ranges. The 4 species were found to segregate spatially into 2 groups, with one group having a significantly shallower core annual depth range than the other. To our knowledge, fine-scale segregation by depth has not been observed previously. Interestingly, the members of each species group appeared complementary, each group comprising species with different dietary preferences and with a larger and smaller body size. An understanding of how core depth ranges differ and how these species utilise vertical habitat could potentially enable geographic ranges around the coast to be predicted, with important implications for how these species interact with fisheries and Marine Protected Areas.

Bacteria produce some of the most potent biomolecules known, of which many cause serious diseases such as tetanus. For prevention, billions of people and countless animals are immunised with the highly effective vaccine, industrially produced by large-scale fermentation. However, toxin production is often hampered by low yields and batch-to-batch variability. Improved productivity has been constrained by a lack of understanding of the molecular mechanisms controlling toxin production. Here we have developed a reproducible experimental framework for screening phenotypic determinants in Clostridium tetani under a process that mimics an industrial setting. We show that amino acid depletion induces production of the tetanus toxin. Using time-course transcriptomics and extracellular metabolomics to generate a ‘fermentation atlas’ that ascribe growth behaviour, nutrient consumption and gene expression to the fermentation phases, we found a subset of preferred amino acids. Exponential growth is characterised by the consumption of those amino acids followed by a slower exponential growth phase where peptides are consumed, and toxin is produced. The results aim at assisting in fermentation medium design towards the improvement of vaccine production yields and reproducibility. In conclusion, our work not only provides deep fermentation dynamics but represents the foundation for bioprocess design based on C. tetani physiological behaviour under industrial settings.

Rhythmic activity patterns are ubiquitous in animals and in the marine environment a dominant rhythmic activity is the diel vertical migration (DVM) of pelagic organisms, moving or ‘migrating’ from deep waters during the day to shallower waters at night. While this overall pattern of movement is well understood, the cryptic nature of the marine environment has limited the study of fine-scale movements within each phase. Active pelagic predators, such as tuna, perform consistent, predictable large-scale vertical movements; however, the fine-scale movements nested within these larger movements have not previously been investigated in detail. Further, the prey field densities are known to differ significantly between day and night, presenting an opportunity to study differences in foraging patterns between these two phases. Here, using long-term depth time series recorded from 93 bigeye tuna, Thunnus obesus , with electronic tags (18 003 days of data), fine-scale changes in vertical movement patterns between day and night time phases were investigated in the context of the Levy foraging hypothesis, which predicts a Levy distribution of move steps during foraging when prey is scarce, but an exponential distribution when prey is abundant and searching is not required. During the day, T. obesus were found to exhibit scale-free movements well fitted by a Levy distribution indicating optimized searching for sparsely distributed prey. During night-time hours, however, exponentially distributed scale-dependent move step lengths were found to be dominant, supporting a simple, Brownian, movement pattern sufficient where prey is abundant. This study not only confirms the predictions of the Levy foraging hypothesis but suggests that the identification of Levy patterns in movement data can be a useful indicator of foraging activity in animals that are difficult to observe directly.

Often the ecology of a commercially fished species and the behaviour of the fishers are inextricably linked. An understanding of both species ecology and fisher behaviour are therefore fundamental for effective fisheries management. In Europe, Rajidae are commercially fished species that are vulnerable to overfishing, have historically been grouped in landings data and declines have been reported to the point of local extinction in some species. Management of these species is therefore important, however an understanding of species ecology and the way they interact with the fishery is lacking. Here we investigate how the differing ecology of four species affects interactions with the fishery by considering gear types, Marine Protected Areas, location of capture and geographic displacements. Our results demonstrate that the four species interacted differently with the fishery, for example Raja clavata were more commonly captured by static nets (69 % of recaptures) and Raja brachyura more commonly by trawlers (77 %). There were clear differences in the location of capture, depths and displacements of the four species resulting in differing interactions with existing management in the form of Marine Protected Areas. For example 53 % of R. clavata recaptures were within the boundaries of an MPA compared to 18 % for R. brachyura. These results provide important differences among species that are generally grouped by current management, emphasising the need for further species specific research to ensure effective management.

Curtobacterium sp. strain SGAir0471 was isolated from tropical air samples collected in Singapore. The genome was assembled using PacBio RS II long reads and Illumina MiSeq short paired-end reads. The complete genome measures 3.53 Mb and consists of 3,151 protein-coding genes, 49 tRNAs, and 12 rRNAs.

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.

Citricoccus sp. strain SGAir0253 was isolated from indoor air collected in Singapore. Its genome sequence was assembled using single-molecule real-time sequencing. It comprises one chromosome of 3.32 Mb and two plasmids of 137 kb and 99 kb. The genome consists of 2,950 protein-coding genes, 49 tRNAs, and 9 rRNAs.

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.

Early circadian studies in plants by de Mairan and de Candolle alluded to a regulation of circadian clocks by humidity. However, this regulation has not been described in detail, nor has its influence on physiology been demonstrated. Here we report that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1. Under simulated natural light and humidity cycles, humidity oscillation increases the amplitude of the circadian clock and further improves plant fitness-related traits. In addition, humidity oscillation enhances effector-triggered immunity at night possibly to counter increased pathogen virulence under high humidity. These results indicate that the humidity oscillation regulates specific circadian outputs besides those co-regulated with the light-dark cycle., Humidity has been shown to influence many aspects of plant physiology. Here Mwimba et al. show that oscillating humidity entrains the circadian clock under constant light conditions and enhances clock amplitude in simulated natural environments, while also improving immunity and overall growth.

SUMMARY Neuronal activity-inducible gene transcription correlates with rapid and transient increases in histone acetylation at promoters and enhancers of activity-regulated genes. Exactly how histone acetylation modulates transcription of these genes has remained unknown. We used single-cell in situ transcriptional analysis to show that Fos and Npas4 are transcribed in stochastic bursts in mouse neurons and that membrane depolarization increases mRNA expression by increasing burst frequency. We then expressed dCas9-p300 or dCas9-HDAC8 fusion proteins to mimic or block activity-induced histone acetylation locally at enhancers. Adding histone acetylation increased Fos transcription by prolonging burst duration and resulted in higher Fos protein levels and an elevation of resting membrane potential. Inhibiting histone acetylation reduced Fos transcription by reducing burst frequency and impaired experience-dependent Fos protein induction in the hippocampus in vivo. Thus, activity-inducible histone acetylation tunes the transcriptional dynamics of experience-regulated genes to affect selective changes in neuronal gene expression and cellular function., In Brief Using CRISPR-mediated epigenome editing, Chen et al. show that enhancer histone acetylation fine-tunes the activity-dependent transcription of Fos in neurons., Graphical Abstract

The thermophilic bacterium Geobacillus thermoleovorans was isolated from a tropical air sample collected in Singapore. The genome was sequenced on the PacBio RS II platform and consists of one chromosome with 3.6 Mb and one plasmid with 75 kb., The thermophilic bacterium Geobacillus thermoleovorans was isolated from a tropical air sample collected in Singapore. The genome was sequenced on the PacBio RS II platform and consists of one chromosome with 3.6 Mb and one plasmid with 75 kb. The genome comprises 3,509 protein-coding genes, 88 tRNAs, and 27 rRNAs.

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., 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.

Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb., Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb. The genome consists of 3,937 protein-coding genes, 86 tRNAs, and 27 rRNAs.

Malarial fever arises from the synchronous bursting of human red blood cells by the Plasmodium parasite. The released parasites re-infect neighboring red blood cells and undergo another asexual cycle of differentiation and proliferation for 48 hours, before again bursting synchronously. The synchrony of bursting is lost during in vitro culturing of the parasite outside the human body, presumably because the asexual cycle is no longer entrained by host-specific circadian cues. Therefore, most in vitro malaria studies have relied on the artificial synchronization of the parasite population. However, much remains unknown about the degree of timing heterogeneity of asexual cycles and how artificial synchronization may affect this timing. Here, we combined time-lapse fluorescence microscopy and long-term culturing to follow single cells and directly measure the heterogeneous timing of in vitro asexual cycles. We first demonstrate that unsynchronized laboratory cultures are not fully asynchronous and the parasites exhibit a bimodal distribution in their first burst times. We then show that synchronized and unsynchronized cultures had similar asexual cycle periods, which indicates that artificial synchronization does not fundamentally perturb asexual cycle dynamics. Last, we demonstrate that sibling parasites descended from the same schizont exhibited significant variation in asexual cycle period, although smaller than the variation between non-siblings. The additional variance between non-siblings likely arises from the variable environments and/or developmental programs experienced in different host cells.

Pseudomonas stutzeri strain SGAir0442 was isolated from tropical air samples collected in Singapore. It is a Gram-negative denitrifying bacterium and an opportunistic human pathogen. Its complete genome consists of one chromosome of 4.52 Mb, containing 4,129 protein-coding genes, 12 rRNA subunits, and 62 tRNAs.

Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the skin microbiome and an opportunistic human pathogen. The strain SGAir0252 was isolated from tropical air samples collected in Singapore, and its complete genome comprises one chromosome of 2.63 Mb and one plasmid of 41.6 kb.

Acinetobacter indicus ( Gammaproteobacteria ) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.

The interaction of two oscillators (cell division cycle and yeast metabolic cycle) with different frequencies is studied. Cell cycle Start is coupled with the initiation of high oxygen consumption and breakdown of storage carbohydrates across diverse strains and different growth rates., Cells have evolved oscillators with different frequencies to coordinate periodic processes. Here we studied the interaction of two oscillators, the cell division cycle (CDC) and the yeast metabolic cycle (YMC), in budding yeast. Previous work suggested that the CDC and YMC interact to separate high oxygen consumption (HOC) from DNA replication to prevent genetic damage. To test this hypothesis, we grew diverse strains in chemostat and measured DNA replication and oxygen consumption with high temporal resolution at different growth rates. Our data showed that HOC is not strictly separated from DNA replication; rather, cell cycle Start is coupled with the initiation of HOC and catabolism of storage carbohydrates. The logic of this YMC–CDC coupling may be to ensure that DNA replication and cell division occur only when sufficient cellular energy reserves have accumulated. Our results also uncovered a quantitative relationship between CDC period and YMC period across different strains. More generally, our approach shows how studies in genetically diverse strains efficiently identify robust phenotypes and steer the experimentalist away from strain-specific idiosyncrasies.

A large, pregnant, female bull shark Carcharhinus leucas was tracked migrating from Seychelles across open ocean to south-east Madagascar, c. 2000 km away, and back again. In Madagascar, the shark spent a prolonged period shallower than 5 m, consistent with entering estuarine habitat to pup, and upon return to Seychelles the shark was slender and no longer gravid. This represents an unprecedented return migration across the open ocean for a C. leucas and highlights the need for international collaboration to manage the regional C. leucas population sustainably.

During bacterial growth, a cell approximately doubles in size prior to division, upon which it splits into two daughter cells. This process is subjected to the inherent perturbations of cellular noise1,2 and thus requires regulation for cell-size homeostasis. The mechanisms underlying cell-size control and their dynamics consequences remain poorly understood due to the difficulty in sizing individual bacteria over long periods of time in a high-throughput manner. Here, we measured and analyzed long-term, single-cell growth and division across different Escherichia coli strains and growth conditions3. We found that a subset of cells in a population exhibited transient oscillations in cell size with periods that stretch across multiple (>10) generations. Our analysis revealed that a simple law governing cell size control – a noisy linear map – explains the origins of these cell-size oscillations across all strains. This noisy linear map implements a negative feedback on cell-size control: a cell with a larger initial size tends to divide earlier, whereas one with a smaller initial size tends to divide later. Combining simulations of cell growth and division with experimental data, we demonstrate that this noisy linear map generates transient oscillations, not just in cell size, but also in constitutive gene expression. Our work provides new insights into the dynamics of bacterial cell-size regulation with implications for the physiological processes involved.