New and Notable This Week

This week’s selection of recently published papers from MDPI journals.

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Design of Catalytically Amplified Sensors for Small Molecules

Abstract: Catalytically amplified sensors link an allosteric analyte binding site with a reactive site to catalytically convert substrate into colored or fluorescent product that can be easily measured. Such an arrangement greatly improves a sensor’s detection limit as illustrated by successful application of ELISA-based approaches. The ability to engineer synthetic catalytic sites into non-enzymatic proteins expands the repertoire of analytes as well as readout reactions. Here we review recent examples of small molecule sensors based on allosterically controlled enzymes and organometallic catalysts. The focus of this paper is on biocompatible, switchable enzymes regulated by small molecules to track analytes both in vivo and in the environment.

For open-access article, see: Makhlynets, O.V.; Korendovych, I.V. Design of Catalytically Amplified Sensors for Small MoleculesBiomolecules 20144, 402-418.

 

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Superresolution Imaging of Human Cytomegalovirus vMIA Localization in Sub-Mitochondrial Compartments

Abstract: The human cytomegalovirus (HCMV) viral mitochondria-localized inhibitor of apoptosis (vMIA) protein, traffics to mitochondria-associated membranes (MAM), where the endoplasmic reticulum (ER) contacts the outer mitochondrial membrane (OMM). vMIA association with the MAM has not been visualized by imaging. Here, we have visualized this by using a combination of confocal and superresolution imaging. Deconvolution of confocal microscopy images shows vMIA localizes away from mitochondrial matrix at the Mitochondria-ER interface. By gated stimulated emission depletion (GSTED) imaging, we show that along this interface vMIA is distributed in clusters. Through multicolor, multifocal structured illumination microscopy (MSIM), we find vMIA clusters localize away from MitoTracker Red, indicating its OMM localization. GSTED and MSIM imaging show vMIA exists in clusters of ~100–150 nm, which is consistent with the cluster size determined by Photoactivated Localization Microscopy (PALM). With these diverse superresolution approaches, we have imaged the clustered distribution of vMIA at the OMM adjacent to the ER. Our findings directly compare the relative advantages of each of these superresolution imaging modalities for imaging components of the MAM and sub-mitochondrial compartments. These studies establish the ability of superresolution imaging to provide valuable insight into viral protein location, particularly in the sub-mitochondrial compartments, and into their clustered organization.

For open-access article, see: Bhuvanendran, S.; Salka, K.; Rainey, K.; Sreetama, S.C.; Williams, E.; Leeker, M.; Prasad, V.; Boyd, J.; Patterson, G.H.; Jaiswal, J.K.; Colberg-Poley, A.M. Superresolution Imaging of Human Cytomegalovirus vMIA Localization in Sub-Mitochondrial CompartmentsViruses 20146, 1612-1636.

 

 

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Quantifying Unique Information

Abstract: We propose new measures of shared information, unique information and synergistic information that can be used to decompose the mutual information of a pair of random variables (Y, Z) with a third random variable X. Our measures are motivated by an operational idea of unique information, which suggests that shared information and unique information should depend only on the marginal distributions of the pairs (X, Y) and (X,Z). Although this invariance property has not been studied before, it is satisfied by other proposed measures of shared information. The invariance property does not uniquely determine our new measures, but it implies that the functions that we define are bounds to any other measures satisfying the same invariance property. We study properties of our measures and compare them to other candidate measures.

For open-access article, see: Bertschinger, N.; Rauh, J.; Olbrich, E.; Jost, J.; Ay, N. Quantifying Unique InformationEntropy 201416, 2161-2183.

 

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Recent Developments in Microbiological Approaches for Securing Mine Wastes and for Recovering Metals from Mine Waters

Abstract: Mining of metals and coals generates solid and liquid wastes that are potentially hazardous to the environment. Traditional methods to reduce the production of pollutants from mining and to treat impacted water courses are mostly physico-chemical in nature, though passive remediation of mine waters utilizes reactions that are catalysed by microorganisms. This paper reviews recent advances in biotechnologies that have been proposed both to secure reactive mine tailings and to remediate mine waters. Empirical management of tailings ponds to promote the growth of micro-algae that sustain populations of bacteria that essentially reverse the processes involved in the formation of acid mine drainage has been proposed. Elsewhere, targeted biomineralization has been demonstrated to produce solid products that allow metals present in mine waters to be recovered and recycled, rather than to be disposed of in landfill.

For open-access article, see: Johnson, D.B. Recent Developments in Microbiological Approaches for Securing Mine Wastes and for Recovering Metals from Mine WatersMinerals 20144, 279-292.

Posted in Biomolecules, Entropy, Life Sciences, Minerals, New and Notable, Viruses.

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