Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans

IntroductionNitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth’s ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions.MethodsIn this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria.Results and DiscussionOur tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment

The uniquely Singapore race : a promotional campaign for the "Uniquely Singapore" brand.

The Uniquely Singapore Race is a brand communications project for Singapore Tourism Board (STB) which aims to communicate the "Uniquely Singapore" brand to youths 18 to 26 years old in polytechnnics and universities of Singapore.Bachelor of Communication Studie

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments

Enzyme Method-Based Microfluidic Chip for the Rapid Detection of Copper Ions

Metal ions in high concentrations can pollute the marine environment. Human activities and industrial pollution are the causes of Cu2+ contamination. Here, we report our discovery of an enzyme method-based microfluidic that can be used to rapidly detect Cu2+ in seawater. In this method, Cu2+ is reduced to Cu+ to inhibit horseradish peroxidase (HRP) activity, which then results in the color distortion of the reaction solution. The chip provides both naked eye and spectrophotometer modalities. Cu2+ concentrations have an ideal linear relationship, with absorbance values ranging from 3.91 nM to 256 μM. The proposed enzyme method-based microfluidic chip detects Cu2+ with a limit of detection (LOD) of 0.87 nM. Other common metal ions do not affect the operation of the chip. The successful detection of Cu2+ was achieved using three real seawater samples, verifying the ability of the chip in practical applications. Furthermore, the chip realizes the functions of two AND gates in series and has potential practical implementations in biochemical detection and biological computing

Enzyme Method-Based Microfluidic Chip for the Rapid Detection of Copper Ions

Metal ions in high concentrations can pollute the marine environment. Human activities and industrial pollution are the causes of Cu2+ contamination. Here, we report our discovery of an enzyme method-based microfluidic that can be used to rapidly detect Cu2+ in seawater. In this method, Cu2+ is reduced to Cu+ to inhibit horseradish peroxidase (HRP) activity, which then results in the color distortion of the reaction solution. The chip provides both naked eye and spectrophotometer modalities. Cu2+ concentrations have an ideal linear relationship, with absorbance values ranging from 3.91 nM to 256 μM. The proposed enzyme method-based microfluidic chip detects Cu2+ with a limit of detection (LOD) of 0.87 nM. Other common metal ions do not affect the operation of the chip. The successful detection of Cu2+ was achieved using three real seawater samples, verifying the ability of the chip in practical applications. Furthermore, the chip realizes the functions of two AND gates in series and has potential practical implementations in biochemical detection and biological computing

Limited effects of depth (0–80 cm) on communities of archaea, bacteria and fungi in paddy soil profiles

Most current microbial studies in paddy soils have focused on the top (0–20 cm) layer where rice roots are concentrated. To better understand the vertical distribution of microorganisms in paddy soils, we investigated the abundances, diversities and community compositions of archaea, bacteria and fungi in six geographically and climatically distinct paddy soil profiles from 0–80-cm depth. Although microbial abundances and operational taxonomic unit (OTU) diversities largely decreased with soil depth, only the community composition of archaea (not bacteria or fungi) was associated with soil depth, echoing that only one archaeal OTU, but no bacterial or fungal OTUs, differed significantly in relative abundance between depth intervals. Mean annual temperature, precipitation and soil iron and manganese concentrations were significantly correlated with the ordinations of microbial communities for all three domains. Besides these common environmental factors, bacterial and archaeal community structures were also influenced by soil chloride and sulphate concentrations, whereas the concentrations of organic matter and total nitrogen were important explanatory factors for the variation in fungal community composition. Further analyses on putative bacterial functions showed significant differences between sampling sites rather than depth intervals, and suggested that bacterial OTUs that significantly varied in relative abundance across sampling sites might be functionally related to organic matter decomposition, sulphur oxidation and reduction, as well as nitrate reduction. Altogether, in the studied paddy soil profiles, the community composition and putative functions of bacteria were largely the same between different vertical layers, each with a thickness of 20 cm. This study suggests that the community compositions of archaea, bacteria and fungi are mainly driven by different soil chemical properties rather than soil depth, which could be linked to the ecological traits of the three microbial domains

Intraplaque stretch in carotid atherosclerotic plaque--an effective biomechanical predictor for subsequent cerebrovascular ischemic events.

BACKGROUND: Stretch is a mechanical parameter, which has been proposed previously to affect the biological activities in different tissues. This study explored its utility in determining plaque vulnerability. METHODS: One hundred and six patients with mild to moderate carotid stenosis were recruited in this study (53 symptomatic and 53 asymptomatic). High resolution, multi-sequence magnetic resonance (MR) imaging was performed to delineate various plaque components. Finite element method was used to predict high stretch concentration within the plaque. RESULTS: During a two-year follow-up, 11 patients in symptomatic group and 3 in asymptomatic group experienced recurrent cerebrovascular events. Plaque stretch at systole and stretch variation during one cardiac cycle was greater in symptomatic group than those in the asymptomatic. Within the symptomatic group, a similar trend was observed in patients with recurrent events compared to those without. CONCLUSION: Plaques with high stretch concentration and large stretch variation are associated with increased risk of future cerebrovascular events

<b>Hydrophobic bulk conservation</b><b> and genetic code determine </b><b>the pattern of </b><b>prokaryotic</b><b> genome</b><b> </b><b>organization</b><b>.</b>

Prokaryotic genomes in general exhibit marked organizational asymmetry, and differ substantially in GC-skew, AT-skew, and GS-bias (gene strand bias). Despite enigmatic origins, these organizational features and genomic GC-content have been described to be widely associated with each other recently, providing an opportunity to probe the evolutionary mechanisms. By analyzing sequence data of 4,012 leading strands from all available representative genomes, we found that the unusual nucleotide usage of coding genes under low GC-content contributed to a shift between two organizational patterns in the context of mutational biases. Analysis of artificially established neutral and natural models further suggests that in genes both GC-skew and AT-skew increase with decreasing GC-content, mostly contributed by synonymous substitutions because of genetic code, and by nonsynonymous substitutions because of hydrophobic bulk conservation in amino acid usage, respectively. This novel mechanistic framework in our study highlights the importance of evolutionary processes “operating at lower levels of organization” in the microbial world.</p

The comparison of plaque stretch (Stretch-P₁) and its variation in different patient groups (A: Stretch-P₁ at diastole and systole of asymptomatic and symptomatic patients; B: the variation of Stretch-P₁ during one cardiac cycle of asymptomatic and symptomatic patients; C: Stretch-P₁ at diastole and systole of patients in subgroups of with and without experiencing recurrent ischaemic cerebrovascular events; D: the variation of Stretch-P₁ during one cardiac cycle of patients in these two subgroups).

<p>The comparison of plaque stretch (Stretch-P₁) and its variation in different patient groups (A: Stretch-P₁ at diastole and systole of asymptomatic and symptomatic patients; B: the variation of Stretch-P₁ during one cardiac cycle of asymptomatic and symptomatic patients; C: Stretch-P₁ at diastole and systole of patients in subgroups of with and without experiencing recurrent ischaemic cerebrovascular events; D: the variation of Stretch-P₁ during one cardiac cycle of patients in these two subgroups).</p

Patient demography.

*<p>Two-sided p value using Fisher's exact test.</p>‡<p>Two-tailed p value using Student t test.</p>†<p>Two-tailed p value using Mann-Whitney test.</p>§<p>ECST defined stenosis.</p