G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum.

Funder: Hong Kong PhD Fellowship SchemeFunder: Hong Kong Special Administrative Region GovernmentG-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.UK Medical Research Council [grants MR/K000535/1 and MR/L008823/1] to CJM. Shenzhen Basic Research Project [JCYJ20180507181642811], Research Grants Council of the Hong Kong SAR, China Projects [CityU 11100421, CityU 11101519, CityU 11100218, N_CityU110/17, CityU 21302317], Croucher Foundation [Project No. 9500030, 9509003], State Key Laboratory of Marine Pollution Director Discretionary Fund, City University of Hong Kong [projects 6000711, 7005503, 9667222, 9680261] to CKK. A generous donation from Mr. and Mrs. Sunny Yang, the University Grants Committee Area of Excellence Scheme (AoE/M-403/16), and the Innovation and Technology Commission, Hong Kong Special Administrative Region Government to the State Key Laboratory of Agrobiotechnology (CUHK) to TFC. EYCC was supported by the Hong Kong PhD Fellowship Scheme

Next-generation analysis of trypanosomatid genome stability and instability

No abstract available

Crystallization by particle attachment in synthetic, biogenic, and geologic environments.

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments

Mechanisms of NK Cell-Macrophage Bacillus anthracis Crosstalk: A Balance between Stimulation by Spores and Differential Disruption by Toxins

NK cells are important immune effectors for preventing microbial invasion and dissemination, through natural cytotoxicity and cytokine secretion. Bacillus anthracis spores can efficiently drive IFN-γ production by NK cells. The present study provides insights into the mechanisms of cytokine and cellular signaling that underlie the process of NK-cell activation by B. anthracis and the bacterial strategies to subvert and evade this response. Infection with non-toxigenic encapsulated B. anthracis induced recruitment of NK cells and macrophages into the mouse draining lymph node. Production of edema (ET) or lethal (LT) toxin during infection impaired this cellular recruitment. NK cell depletion led to accelerated systemic bacterial dissemination. IFN-γ production by NK cells in response to B. anthracis spores was: i) contact-dependent through RAE-1-NKG2D interaction with macrophages; ii) IL-12, IL-18, and IL-15-dependent, where IL-12 played a key role and regulated both NK cell and macrophage activation; and iii) required IL-18 for only an initial short time window. B. anthracis toxins subverted both NK cell essential functions. ET and LT disrupted IFN-γ production through different mechanisms. LT acted both on macrophages and NK cells, whereas ET mainly affected macrophages and did not alter NK cell capacity of IFN-γ secretion. In contrast, ET and LT inhibited the natural cytotoxicity function of NK cells, both in vitro and in vivo. The subverting action of ET thus led to dissociation in NK cell function and blocked natural cytotoxicity without affecting IFN-γ secretion. The high efficiency of this process stresses the impact that this toxin may exert in anthrax pathogenesis, and highlights a potential usefulness for controlling excessive cytotoxic responses in immunopathological diseases. Our findings therefore exemplify the delicate balance between bacterial stimulation and evasion strategies. This highlights the potential implication of the crosstalk between host innate defences and B. anthracis in initial anthrax control mechanisms

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public. In a context in which animal and human health are intertwined aspects of the one-health concept it is of utmost importance to define the markers of stress and welfare. These are important tools for producers, retailers, regulatory agents and ultimately consumers to effectively monitor and assess the welfare state of production animals. Proteomics is the science that studies the proteins existing in a given tissue or fluid. In this review we address this topic by showing clear examples where proteomics has been used to study stress-induced changes at various levels. We adopt a multi-species (cattle, swine, small ruminants, poultry, fish and shellfish) approach under the effect of various stress inducers (handling, transport, management, nutritional, thermal and exposure to pollutants) clearly demonstrating how proteomics and systems biology are key elements to the study of stress and welfare in farm animals and powerful tools for animal welfare, health and productivity

Design process and simulation testing of a shape memory alloy actuated robotic microgripper

Microgrippers are commonly used for micromanipulation of micro-objects with dimensions from 1 to 100 µm and attain features of reliable accuracy, low cost, wide jaw aperture and variable applied force. This paper studies the design process, simulation, and testing of a microgripper which can manipulate and assemble a platinum resistance temperature probe, made from a 25 µm diameter platinum wire, a 20 mm diameter tinned copper wire, and a printed circuit board type connector. Various microgripper structures and actuator types were researched and reviewed to determine the most suitable design for the required micromanipulation task. Operation tests using SolidWorks and ANSYS software were conducted to test a parallelogram structure with flexible single-notch hinges. The best suited material was found to be Aluminium alloy 7075-T6 as it was capable of producing a large jaw tip displacement of 0.7 mm without exceeding its tensile yield strength limit. A shape memory alloy was chosen as a choice of actuator to close the microgripper jaws. To ensure a repeatably accurate datum point, the final microgripper consisted of a fixed arm and a flexible arm. An optimisation process using ANSYS studied the hinge thickness and radius dimensions of the microgripper which improved its deflection whilst reducing the experienced stress

Controlling and characterising the deposits from polymer droplets containing microparticles and salt

It is very well known that as suspension droplets evaporate, a pinned contact line leads to strong outwards capillary flow resulting in a robust coffee ring-stain at the periphery of the droplet. Conversely tall pillars are deposited in the centre of the droplet when aqueous droplets of poly(ethylene oxide) evaporate following a boot-strapping process in which the contact line undergoes fast receding, driven by polymer precipitation. Here we map out the phase behaviour of a combined particle-polymer system, illustrating a range of final deposit shapes, from ring-stain to flat deposit to pillar. Deposit topologies are measured using profile images and stylus profilometery, and characterised using the skewness of the profile as a simple analytic method for quantifying the shapes: pillars produce positive skew, flat deposits have zero skew and ring-stains have a negative value. We also demonstrate that pillar formation can be disrupted using potassium sulphate salt solutions, which change the water from a good solvent to a thetapoint solvent, consequently reducing the size of the polymer coils. This inhibits polymer crystallisation, interfering with the bootstrap process and ultimately preventing pillars from forming. Again, the deposit shapes are quantified using the skew parameter