A new twist on PIFE: photoisomerisation-related fluorescence enhancement

PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule and, in this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turn PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.Comment: No Comment

Intrinsic defect engineering of CVD grown monolayer MoS2_2 for tuneable functional nanodevices

Defects in atomically thin materials can drive new functionalities and expand applications to multifunctional systems that are monolithically integrated. An ability to control formation of defects during the synthesis process is an important capability to create practical deployment opportunities. Molybdenum disulfide (MoS$_2$), a two-dimensional (2D) semiconducting material harbors intrinsic defects that can be harnessed to achieve tuneable electronic, optoelectronic, and electrochemical devices. However, achieving precise control over defect formation within monolayer MoS$_2$, while maintaining the structural integrity of the crystals remains a notable challenge. Here, we present a one-step, in-situ defect engineering approach for monolayer MoS$_2$ using a pressure dependent chemical vapour deposition (CVD) process. Monolayer MoS$_2$ grown in low-pressure CVD conditions (LP-MoS$_2$) produces sulfur vacancy (Vs) induced defect rich crystals primarily attributed to the kinetics of the growth conditions. Conversely, atmospheric pressure CVD grown MoS$_2$ (AP-MoS$_2$) passivates these Vs defects with oxygen. This disparity in defect profiles profoundly impacts crucial functional properties and device performance. AP-MoS$_2$ shows a drastically enhanced photoluminescence, which is significantly quenched in LP-MoS$_2$ attributed to in-gap electron donor states induced by the Vs defects. However, the n-doping induced by the Vs defects in LP-MoS$_2$ generates enhanced photoresponsivity and detectivity in our fabricated photodetectors compared to the AP-MoS$_2$ based devices. Defect-rich LP-MoS$_2$ outperforms AP-MoS$_2$ as channel layers of field-effect transistors (FETs), as well as electrocatalytic material for hydrogen evolution reaction (HER). This work presents a single-step CVD approach for in-situ defect engineering in monolayer MoS$_2$ and presents a pathway to control defects in other monolayer material systems.Comment: 29 pages, 5 figure

A new twist on PIFE: photoisomerisation-related fluorescence enhancement

PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule and, in this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turn PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules

The Extended Solar Cycle: Muddying the Waters of Solar/Stellar Dynamo Modeling or Providing Crucial Observational Constraints?

In 1844 Schwabe discovered that the number of sunspots increased and decreased over a period of about 11 years, that variation became known as the sunspot cycle. Almost eighty years later, Hale described the nature of the Sun's magnetic field, identifying that it takes about 22 years for the Sun's magnetic polarity to cycle. It was also identified that the latitudinal distribution of sunspots resembles the wings of a butterfly—showing migration of sunspots in each hemisphere that abruptly start at mid-latitudes (about ±35o) toward the Sun's equator over the next 11 years. These sunspot patterns were shown to be asymmetric across the equator. In intervening years, it was deduced that the Sun (and sun-like stars) possess magnetic activity cycles that are assumed to be the physical manifestation of a dynamo process that results from complex circulatory transport processes in the star's interior. Understanding the Sun's magnetism, its origin and its variation, has become a fundamental scientific objective—the distribution of magnetism, and its interaction with convective processes, drives various plasma processes in the outer atmosphere that generate particulate, radiative, eruptive phenomena, and shape the heliosphere. In the past few decades, a range of diagnostic techniques have been employed to systematically study finer scale magnetized objects, and associated phenomena. The patterns discerned became known as the “Extended Solar Cycle” (ESC). The patterns of the ESC appeared to extend the wings of the activity butterfly back in time, nearly a decade before the formation of the sunspot pattern, and to much higher solar latitudes. In this short review, we describe their observational patterns of the ESC and discuss possible connections to the solar dynamo as we depart on a multi-national collaboration to investigate the origins of solar magnetism through a blend of archived and contemporary data analysis with the goal of improving solar dynamo understanding and modeling

Transcription initiation at a consensus bacterial promoter proceeds via a 'bind-unwind-load-and-lock' mechanism

Transcription initiation starts with unwinding of promoter DNA by RNA polymerase (RNAP) to form a catalytically competent RNAP-promoter complex (RPO). Despite extensive study, the mechanism of promoter unwinding has remained unclear, in part due to the transient nature of intermediates on path to RPo. Here, using single-molecule unwinding-induced fluorescence enhancement to monitor promoter unwinding, and single-molecule fluorescence resonance energy transfer to monitor RNAP clamp conformation, we analyze RPo formation at a consensus bacterial core promoter. We find that the RNAP clamp is closed during promoter binding, remains closed during promoter unwinding, and then closes further, locking the unwound DNA in the RNAP active-centre cleft. Our work defines a new, 'bind-unwind-load-and-lock' model for the series of conformational changes occurring during promoter unwinding at a consensus bacterial promoter and provides the tools needed to examine the process in other organisms and at other promoters

A peptide-based synthetic transcription factor selectively activates transcription in a mammalian cell

A peptide-based cell permeable synthetic transcription factor is reported, which binds to its target site with high affinity and specificity. When linked to a HAT-binding peptide, it causes significant upregulation of gene expression in a mammalian cell. Such molecules may be developed for selectively activating repressed genes in mammalian cells

Psilorhynchus kamengensis, a new species of fish (Teleostei: Psilorhynchidae) from northeast India

Psilorhynchus kamengensis, new species, is described from a stream of the Kameng River, a northern tributary to the Brahmaputra drainage, Arunachal Pradesh, northeast India. The new species belongs to the P. balitora species group and can be distinguished from all other members of this group by the presence of a longer post-epiphyseal fontanelle, 3 unbranched anal-fin rays, 9 + 8 caudal-fin rays, 35 vertebrae and fin coloration. The validity of the species is also corroborated by molecular phylogenetic analysis based on the mitochondrial cyt b gene

A Synthetic Peptide Mimic of λ-Cro shows Sequence-Specific Binding <i>in Vitro</i> and <i>in Vivo</i>

Development of small synthetic transcription factors is important for future cellular engineering and therapeutics. This article describes the chemical synthesis of α-amino-isobutyric acid (Aib) substituted, conformationally constrained, helical peptide mimics of <i>Cro</i> protein from bacteriophage λ that encompasses the DNA recognition elements. The Aib substituted constrained helical peptide monomer shows a moderately reduced dissociation constant compared to the corresponding unsubstituted wild type peptide. A suitably cross-linked dimeric version of the peptide, mimicking the dimeric protein, recapitulates some of the important features of <i>Cro</i>. It binds to the operator site O_R3, a high affinity <i>Cro</i> binding site in the λ genome, with good affinity and single base-pair discrimination specificity. A dimeric version of an even shorter peptide mimic spanning only the recognition helix of the helix-turn-helix motif of the <i>Cro</i> protein was created following the same design principles. This dimeric peptide binds to O_R3 with affinity greater than that of the longer version. Chemical shift perturbation experiments show that the binding mode of this peptide dimer to the cognate operator site sequence is similar to the wild type <i>Cro</i> protein. A Green Fluorescent Protein based reporter assay <i>in vivo</i> reveals that the peptide dimer binds the operator site sequences with considerable selectivity and inhibits gene expression. Peptide mimics designed in this way may provide a future framework for creating effective synthetic transcription factors