RS-FISH: Precise, interactive, fast, and scalable FISH spot detection

Fluorescent in-situ hybridization (FISH)-based methods are powerful tools to study molecular processes with subcellular resolution, relying on accurate identification and localization of diffraction-limited spots in microscopy images. We developed the Radial Symmetry-FISH (RS-FISH) software that accurately, robustly, and quickly detects single-molecule spots in two and three dimensions, making it applicable to several key assays, including single-molecule FISH (smFISH), spatial transcriptomics, and spatial genomics. RS-FISH allows interactive parameter tuning and scales to large sets of images as well as tera-byte sized image volumes such as entire brain scans using straight-forward distributed processing on workstations, clusters, and in the cloud

RS-FISH: precise, interactive, fast, and scalable FISH spot detection

Fluorescent in-situ hybridization (FISH)-based methods extract spatially resolved genetic and epigenetic information from biological samples by detecting fluorescent spots in microscopy images, an often challenging task. We present Radial Symmetry-FISH (RS-FISH), an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. RS-FISH offers interactive parameter tuning and readily scales to large datasets and image volumes of cleared or expanded samples using distributed processing on workstations, clusters, or the cloud. RS-FISH maintains high detection accuracy and low localization error across a wide range of signal-to-noise ratios, a key feature for single-molecule FISH, spatial transcriptomics, or spatial genomics applications

Possible origins of macroscopic left-right asymmetry in organisms

I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "right-hand rule"; at the microscopic level, the cell's cytoskeleton of chiral filaments seems always to be involved, usually in collective states driven by polymerization forces or molecular motors. It seems particularly easy for handedness to emerge in a shear or rotation in the background of an effectively two-dimensional system, such as the cell membrane or a layer of cells, as this requires no pre-existing axis apart from the layer normal. I detail a scenario involving actin/myosin layers in snails and in C. elegans, and also one about the microtubule layer in plant cells. I also survey the other examples that I am aware of, such as the emergence of handedness such as the emergence of handedness in neurons, in eukaryote cell motility, and in non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue. Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec

Fractionation of a Herbal Antidiarrheal Medicine Reveals Eugenol as an Inhibitor of Ca2+-Activated Cl− Channel TMEM16A

The Ca2+-activated Cl− channel TMEM16A is involved in epithelial fluid secretion, smooth muscle contraction and neurosensory signaling. We identified a Thai herbal antidiarrheal formulation that inhibited TMEM16A Cl− conductance. C18-reversed-phase HPLC fractionation of the herbal formulation revealed >98% of TMEM16A inhibition activity in one out of approximately 20 distinct peaks. The purified, active compound was identified as eugenol (4-allyl-2-methoxyphenol), the major component of clove oil. Eugenol fully inhibited TMEM16A Cl− conductance with single-site IC50∼150 µM. Eugenol inhibition of TMEM16A in interstitial cells of Cajal produced strong inhibition of intestinal contraction in mouse ileal segments. TMEM16A Cl− channel inhibition adds to the list of eugenol molecular targets and may account for some of its biological activities

Using an on-line image analysis technique to characterize sucrose crystal morphology during a crystallization run

The morphological forms and habits of crystals and agglomeration are important properties on crystallization processes. Online techniques for realtime measurement of these properties are mandatory for a better comprehension of crystal growth phenomenon. The present paper presents and describes a new online method to determine the complexity level of a crystal or a population of crystals during a crystallization process. An image analysis technique is combined with discriminant factorial analysis leading to results that allow the computation of the complexity of crystals through the parameter agglomeration degree of crystals. With this methodology, it has been possible to distinguish online and automatically among three different classes of crystals according to their complexity. It further describes the application of such methodology on the study of CaCl2, D-fructose, and D-glucose influence on the crystallization of sucrose, namely, on crystal size, morphology, and complexity. The effect of supersaturation, growth rate, and impurity concentration on the type, amount, and complexity level of the agglomerates was determined at different temperatures. The combination of image analysis and kinetic results allowed to understand better the crystallization phenomena in the presence and absence of impurities. The image analysis results suggest the possible application of this tool for process control, optimizing, by this way, laboratory and industrial crystallizers.This work was supported by Fundacao para a Ciencia e Tecnologia under program contract numbers SFRH/BD/11315/2002 and SFRH/BPD/45637/2008

Mutations Altering the Interplay between GkDnaC Helicase and DNA Reveal an Insight into Helicase Unwinding

Replicative helicases are essential molecular machines that utilize energy derived from NTP hydrolysis to move along nucleic acids and to unwind double-stranded DNA (dsDNA). Our earlier crystal structure of the hexameric helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in complex with single-stranded DNA (ssDNA) suggested several key residues responsible for DNA binding that likely play a role in DNA translocation during the unwinding process. Here, we demonstrated that the unwinding activities of mutants with substitutions at these key residues in GkDnaC are 2–4-fold higher than that of wild-type protein. We also observed the faster unwinding velocities in these mutants using single-molecule experiments. A partial loss in the interaction of helicase with ssDNA leads to an enhancement in helicase efficiency, while their ATPase activities remain unchanged. In strong contrast, adding accessory proteins (DnaG or DnaI) to GkDnaC helicase alters the ATPase, unwinding efficiency and the unwinding velocity of the helicase. It suggests that the unwinding velocity of helicase could be modulated by two different pathways, the efficiency of ATP hydrolysis or protein-DNA interaction

Rapid Transcriptional Pulsing Dynamics of High Expressing Retroviral Transgenes in Embryonic Stem Cells

Single cell imaging studies suggest that transcription is not continuous and occurs as discrete pulses of gene activity. To study mechanisms by which retroviral transgenes can transcribe to high levels, we used the MS2 system to visualize transcriptional dynamics of high expressing proviral integration sites in embryonic stem (ES) cells. We established two ES cell lines each bearing a single copy, self-inactivating retroviral vector with a strong ubiquitous human EF1α gene promoter directing expression of mRFP fused to an MS2-stem-loop array. Transfection of MS2-EGFP generated EGFP focal dots bound to the mRFP-MS2 stem loop mRNA. These transcription foci colocalized with the transgene integration site detected by immunoFISH. Live tracking of single cells for 20 minutes detected EGFP focal dots that displayed frequent and rapid fluctuations in transcription over periods as short as 25 seconds. Similarly rapid fluctuations were detected from focal doublet signals that colocalized with replicated proviral integration sites by immunoFISH, consistent with transcriptional pulses from sister chromatids. We concluded that retroviral transgenes experience rapid transcriptional pulses in clonal ES cell lines that exhibit high level expression. These events are directed by a constitutive housekeeping gene promoter and may provide precedence for rapid transcriptional pulsing at endogenous genes in mammalian stem cells

Advancing international human resource management scholarship on paternalistic leadership and gender: the contribution of postcolonial feminism

This article aims to inspire international human resource management (IHRM) scholarship that incorporates postcolonial feminist theory, using the under-researched topic of paternalistic leadership and gender to illustrate the opportunities and challenges such an endeavour can present. Paternalistic leadership is utilised because it represents one of the most widely used indigenous frameworks for examining leadership in Chinese contexts. The principal theoretical contribution of this article centres on providing IHRM scholars with postcolonial feminist ideas, perspectives and sites of inquiry for cultivating future research on gender and paternalistic leadership. The salience of postcolonial feminism resides in its capacity to address the representation of non-western women in feminist theory as a universal, transhistorical category, to centralise cultural difference in theorising gender, to shatter binaries reproduced by colonialism and imperialism (e.g. ‘West/East’, 'Western/Third World Woman') and to generate indigenous, localised knowledge on non-western women. Three sites of inquiry are discussed: 1) Chinese feminisms and genders; 2) Chinese cultures and gender norms; 3) voice, agency and the subaltern woman. This article provides research propositions for IHRM scholars seeking to translate postcolonial feminist ideas into empirical research. The article concludes by outlining implications for practice and providing research questions to guide future IHRM scholarship