Performing multispecies studies in Southern Africa: historical legacies, marginalised subjects, reflexive positionalities.

Multispecies studies are known for tackling human exceptionalism. Whilst the field has seen a remarkable increase in popularity amongst scholars in the humanities and social sciences, critiques argue that it neglects inequalities and consequential differences amongst humans and between humans and other-than-humans. These critiques are especially relevant in the context of Southern Africa, where extreme inequalities amongst humans persist whilst wildlife is often perceived to enjoy a favoured position in the region's prominent conservation industries.

Triple-Stranded DNA As a Structural Element in DNA Origami.

Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex-triplex DNA motifs as pH-dependent building blocks in DNA origami.

A DNA origami rotary ratchet motor.

To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry.

Antigen-Triggered Logic-Gating of DNA Nanodevices.

Synthetic nanoscale devices that reconfigure dynamically in response to physiological stimuli could offer new avenues for diagnostics and therapy. Here, we report a strategy for controlling the state of DNA nanodevices based on sensing antigens with IgG antibodies. To this end, we use IgG antibodies as structural elements to kinetically trap reconfigurable DNA origami structures in metastable states.

Programmable icosahedral shell system for virus trapping.

Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties.

Advancing Biophysics Using DNA Origami.

DNA origami enables the bottom-up construction of chemically addressable, nanoscale objects with user-defined shapes and tailored functionalities. As such, not only can DNA origami objects be used to improve existing experimental methods in biophysics, but they also open up completely new avenues of exploration. In this review, we discuss basic biophysical concepts that are relevant for prospective DNA origami users.

Programmable Bivalent Peptide-DNA Locks for pH-Based Control of Antibody Activity.

The ability to control antibody activity by pH has important applications in diagnostics, therapeutic antibody targeting, and antibody-guided imaging. Here, we report the rational design of bivalent peptide-DNA ligands that allow pH-dependent control of antibody activity. Our strategy uses a pH-responsive DNA triple helix to control switching from a tight-binding bivalent peptide-DNA lock into a weaker-binding monovalent ligand.

Accelerating DNA-Based Computing on a Supramolecular Polymer.

Dynamic DNA-based circuits represent versatile systems to perform complex computing operations at the molecular level. However, the majority of DNA circuits relies on freely diffusing reactants, which slows down their rate of operation substantially. Here we introduce the use of DNA-functionalized benzene-1,3,5-tricarboxamide (BTA) supramolecular polymers as dynamic scaffolds to template DNA-based molecular computing.

Controlling protein activity by dynamic recruitment on a supramolecular polymer platform.

Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment.

Hierarchical control of enzymatic actuators using DNA-based switchable memories.

Inspired by signaling networks in living cells, DNA-based programming aims for the engineering of biochemical networks capable of advanced regulatory and computational functions under controlled cell-free conditions. While regulatory circuits in cells control downstream processes through hierarchical layers of signal processing, coupling of enzymatically driven DNA-based networks to downstream processes has rarely been reported. Here, we expand the scope of molecular programming by engineering hierarchical control of enzymatic actuators using feedback-controlled DNA-circuits capable of advanced regulatory dynamics.

Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy.

A photocrosslinkable protein G variant was used as an adapter protein to covalently and site-specifically conjugate an antibody and an Fc-fusion protein to an oligonucleotide. This modular approach enables straightforward decoration of DNA nanostructures with complex native proteins while retaining their innate binding affinity, allowing precise control over the nanoscale spatial organization of such proteins for in vitro and in vivo biomedical applications.

DNA-Specific Biosensors Based on Intramolecular β-Lactamase-Inhibitor Complex Formation.

Synthetic protein switches that sequence-specifically respond to oligonucleotide-based input triggers provide valuable tools for the readout of oligonucleotide-based biomolecular systems and networks. Here, we discuss a highly modular approach to reversibly control the DNA-directed assembly and disassembly of a complex between TEM1-β-lactamase and its inhibitor protein BLIP. By conjugating each protein to a unique handle oligonucleotide, the enzyme-inhibitor pair is noncovalently assembled upon the addition of a complementary ssDNA template strand, resulting in inhibition of enzyme activity.

Nucleic acid detection using BRET-beacons based on bioluminescent protein-DNA hybrids.

Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor. While classical molecular beacons are hampered by background fluorescence and scattering, these BRET-beacons allow detection of low pM concentrations of nucleic acids directly in complex media.

Antibody-controlled actuation of DNA-based molecular circuits.

DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically.

DNA-based control of protein activity.

DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed.

eZinCh-2: A Versatile, Genetically Encoded FRET Sensor for Cytosolic and Intraorganelle Zn(2+) Imaging.

Zn(2+) plays essential and diverse roles in numerous cellular processes. To get a better understanding of intracellular Zn(2+) homeostasis and the putative signaling role of Zn(2+), various fluorescent sensors have been developed that allow monitoring of Zn(2+) concentrations in single living cells in real time. Thus far, two families of genetically encoded FRET-based Zn(2+) sensors have been most widely applied, the eCALWY sensors developed by our group and the ZapCY sensors developed by Palmer and co-workers.

DNA-directed control of enzyme-inhibitor complex formation: a modular approach to reversibly switch enzyme activity.

DNA-templated reversible assembly of an enzyme-inhibitor complex is presented as a new and highly modular approach to control enzyme activity. TEM1-β-lactamase and its inhibitor protein BLIP were conjugated to different oligonucleotides, resulting in enzyme inhibition in the presence of template strand. Formation of a rigid dsDNA linker upon addition of a complementary target strand disrupts the enzyme-inhibitor complex and results in the restoration of enzyme activity, enabling detection of as little as 2 fmol DNA.

Analytical model of an isolated single-atom electron source.

An analytical model of a single-atom electron source is presented, where electrons are created by near-threshold photoionization of an isolated atom. The model considers the classical dynamics of the electron just after the photon absorption, i.e.

Ultrafast electron diffraction using an ultracold source.

The study of structural dynamics of complex macromolecular crystals using electrons requires bunches of sufficient coherence and charge. We present diffraction patterns from graphite, obtained with bunches from an ultracold electron source, based on femtosecond near-threshold photoionization of a laser-cooled atomic gas. By varying the photoionization wavelength, we change the effective source temperature from 300 K to 10 K, resulting in a concomitant change in the width of the diffraction peaks, which is consistent with independently measured source parameters.

Effective temperature of an ultracold electron source based on near-threshold photoionization.

We present a detailed description of measurements of the effective temperature of a pulsed electron source, based on near-threshold photoionization of laser-cooled atoms. The temperature is determined by electron beam waist scans, source size measurements with ion beams, and analysis with an accurate beam line model. Experimental data is presented for the source temperature as a function of the wavelength of the photoionization laser, for both nanosecond and femtosecond ionization pulses.

High-coherence electron bunches produced by femtosecond photoionization.

With the development of ultrafast electron and X-ray sources it is becoming possible to study structural dynamics with atomic-level spatial and temporal resolution. Because of their short mean free path, electrons are particularly well suited for investigating surfaces and thin films, such as the challenging and important class of membrane proteins. To perform single-shot diffraction experiments on protein crystals, an ultracold electron source was proposed, based on near-threshold photoionization of laser-cooled atoms, which is capable of producing electron pulses of both high intensity and high coherence.

Effects of micronized fenofibrate and vitamin E on in vitro oxidation of lipoproteins in patients with type 1 diabetes mellitus.

Objective: The primary objective was to compare the antioxidant activity of micronised fenofibrate 200 mg to 400 IU of vitamin E and placebo, on the LDL and VLDL particles of patients with type 1 diabetes. The secondary objective was to investigate the possible synergy between micronized fenofibrate and vitamin E and to compare the efficacy of these treatments on lipids.

Methods: A double-blind, placebo-controlled trial in which patients were randomised into three treatment groups after a wash-out period of 8 weeks: the placebo group (Pla/Pla-group) in which patients received placebo during two consecutive periods of 8 weeks, the vitamin E group (Vit E/Vit E-group) in which patients received Vitamin E during two consecutive periods, and the fenofibrate/Vitamin E group (Fen/Fen + Vit E-group) in which patients received fenofibrate during the first period, followed by fenofibrate and vitamin E during the consecutive period.

Long term magnesium supplementation influences favourably the natural evolution of neuropathy in Mg-depleted type 1 diabetic patients (T1dm).

Chronic Mg depletion in T1dm has been linked to polyneuropathy (PNP). Short term Mg supplementation has suggested a decrease in pathological EMG signs typical for PNP. The aim of this study is to determine if long term supplementation under stable metabolic control can normalize the Mg status and influence the natural evolution of PNP.

Four cases of red blood cell aplasia in association with the use of mycophenolate mofetil in renal transplant patients.

Mycophenolate mofetil (MMF) is one of the new immunosuppressive drugs used in renal transplantation. MMF inhibits the de novo purine synthesis. Since this purine synthesis in lymphocytes entirely depends on the de novo pathway, MMF is considered to cause a selective inhibition of T- and B lymphocytes.

Long-term pharmacologic doses of vitamin E only moderately affect the erythrocytes of patients with type 1 diabetes mellitus.

In erythrocytes from diabetic patients, increased membrane lipid peroxidation might lead to abnormalities in composition and function. To study this relationship, we investigated the effects of a moderate pharmacologic dose of vitamin E for 1 y on erythrocyte membrane peroxidation in vitro and on its fatty acid composition, antioxidant capacity and rheological function. In a random and double-blind manner, type 1 diabetic patients (n = 44) were assigned to the following two groups: Group S received 250 IU (168 mg) d-alpha tocopherol 3 times daily for 1 y.