BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies

Background

The software available to date for analyzing image sequences from time-lapse microscopy works only for certain bacteria and under limited conditions. These programs, mostly MATLAB-based, fail for microbes with irregular shape, indistinct cell division sites, or that grow in closely packed microcolonies. Unfortunately, many organisms of interest have these characteristics, and analyzing their image sequences has been limited to time consuming manual processing.

Results

Here we describe BactImAS – a modular, multi-platform, open-source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time-lapse movies. BactImAS uses a semi-automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The program segments and tracks cells using a newly-developed algorithm designed for movies with difficult-to-segment cells that exhibit small frame-to-frame differences. Measurements are extracted from images in a configurable, automated fashion and an SQLite database is used to store, retrieve, and exchange all acquired data. Finally, the BactImAS can generate configurable lineage tree visualizations and export data as CSV files. We tested BactImAS on time-lapse movies of Mycobacterium smegmatis and achieved at least 10-fold reduction of processing time compared to manual analysis. We illustrate the power of the visualization tool by showing heterogeneity of both icl expression and cell growth atop of a lineage tree.

Conclusions

The presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-251) contains supplementary material, which is available to authorized users.     

Impaired regenerative response of primary sensory neurons in ZPK/DLK gene-trap mice

Rapid and persistent activation of c-JUN is necessary for axonal regeneration after nerve injury, although upstream molecular events leading to c-JUN activation remain largely unknown. ZPK/DLK/MAP3K12 activates the c-Jun N-terminal kinase pathway at an apical level. We investigated axonal regeneration of the dorsal root ganglion (DRG) neurons of homozygous ZPK/DLK gene-trap mice. In vitro neurite extension assays using DRG explants from 14 day-old mice revealed that neurite growth rates of the ZPK/DLK gene-trap DRG explants were reduced compared to those of the wild-type DRG explants. Three ZPK/DLK gene-trap mice which survived into adulthood were subjected to sciatic nerve axotomy. At 24 h after axotomy, phosphorylated c-JUN-positive DRG neurons were significantly less frequent in ZPK/DLK gene-trap mice than in wild-type mice. These results indicate that ZPK/DLK is involved in regenerative responses of mammalian DRG neurons to axonal injury through activation of c-JUN.     

In vivo calcium dynamics during neural crest cell migration and patterning using GCaMP3

Examining calcium dynamics within the neural crest (NC) has the potential to shed light on mechanisms that regulate complex cell migration and patterning events during embryogenesis. Unfortunately, typical calcium indicators are added to culture media or have low signal to noise after microinjection into tissue that severely limit analyses to cultured cells or superficial events. Here, we studied in vivo calcium dynamics during NC cell migration and patterning, using a genetically encoded calcium sensor, GCaMP3. We discovered that trunk NC cells displayed significantly more spontaneous calcium transients than cranial NC cells, and during cell aggregation versus cell migration events. Spontaneous calcium transients were more prevalent during NC cell aggregation into discrete sympathetic ganglia (SG). Blocking of N-cadherin activity in trunk NC cells near the presumptive SG led to a dramatic decrease in the frequency of spontaneous calcium transients. Detailed analysis and mathematical modeling of cell behaviors during SG formation showed NC cells aggregated into clusters after displaying a spontaneous calcium transient. This approach highlights the novel application of a genetically encoded calcium indicator to study subsets of cells during ventral events in embryogenesis.     

Intracellular colocalization of HAP1/STBs with steroid hormone receptors and its enhancement by a proteasome inhibitor

The stigmoid body (STB) is a cytoplasmic inclusion containing huntingtin-associated protein 1 (HAP1), and HAP1/STB formation is induced by transfection of the HAP1 gene into cultured cells. In the present study, we examined the intracellular colocalization of HAP1/STBs with steroid hormone receptors (SHRs), including the androgen receptor (AR), estrogen receptor, glucocorticoid receptor (GR), and mineralocorticoid receptor, in COS-7 cells cotransfected with HAP1 and each receptor. We found that C-terminal ligand-binding domains of all SHRs had potential for colocalization with HAP1/STBs, whereas only AR and GR were clearly colocalized with HAP1/STBs when each full-length SHR was coexpressed with HAP1. In addition, it appeared that HAP1/STBs did not disrupt GR and AR functions because the receptors on HAP1/STBs maintained nuclear translocation activity in response to their specific ligands. When the cells were treated with a proteasome inhibitor, GR and AR localized outside HAP1/STBs translocated into the nucleus, whereas the receptors colocalized with HAP1/STBs persisted in their colocalization even after treatment with their ligands. Therefore, HAP1/STBs may be involved in cytoplasmic modifications of the nuclear translocation of GR and AR in a ubiquitin–proteasome system.     

Role of PI 3-kinase and PIP3 in submandibular gland branching morphogenesis

The mouse submandibular gland (SMG) epithelium undergoes extensive morphogenetic branching during embryonic development as the first step in the establishment of its glandular structure. However, the specific signaling pathways required for SMG branching morphogenesis are not well understood. Using E13 mouse SMG organ cultures, we showed that inhibitors of phosphatidylinositol 3-kinase (PI 3-kinase), wortmannin and LY294002, substantially inhibited branching morphogenesis in SMG. Branching morphogenesis of epithelial rudiments denuded of mesenchyme was inhibited similarly, indicating that PI 3-kinase inhibitors act directly on the epithelium. Immunostaining and Western analysis demonstrated that the p85 isoform of PI 3-kinase is expressed in epithelium at levels higher than in the mesenchyme. A target of PI 3-kinase, Akt/protein kinase B (PKB), showed decreased phosphorylation at Ser(473) by Western analysis in the presence of PI 3-kinase inhibitors. The major lipid product of PI 3-kinase, phosphatidylinositol 3,4,5-trisphosphate (PIP(3)), was added exogenously to SMG via a membrane-transporting carrier in the presence of PI 3-kinase inhibitors and was found to stimulate cleft formation, the first step of branching morphogenesis. Together, these data indicate that PI 3-kinase plays a role in the regulation of epithelial branching morphogenesis in mouse SMG acting through a PIP(3) pathway.     

A role for RhoA in the two-phase migratory pattern of post-otic neural crest cells

Neural crest (NC) cells have been elegantly traced to follow stereotypical migratory pathways throughout the vertebrate embryo, yet we still lack complete information on individual cell migratory behaviors and how molecular mechanisms direct NC cell guidance. Here, we analyze the spatio-temporal migratory pattern of post-otic NC and the in vivo role of the small Rho GTPase, RhoA, using fluorescent cell labeling, molecular perturbation, and intravital 4D (3D+ time) confocal imaging in the intact chick embryo. We find that the post-otic NC cell migratory pattern is established in two phases with distinct cell migratory behaviors. An initial wide front of lateral-directed NC cells, led by NC from rhombomere 7 (r7), move as a distinct subpopulation. This is followed in time by fewer NC cells that migrate collectively from r7 to r8 in a follow-the-leader manner with extensive cellular extensions between cells. We show that post-otic migratory NC cells express RhoA, using RT-PCR on isolated, flow cytometry sorted NC cells and in neural tube culture explants. When RhoA function is altered by expression of a dominant negative or constitutively active form, or injection of C3, there are two major consequences. RhoA constitutively active expressing NC cells are less directional, slower and form fewer follow-the-leader chain assemblies. NC cells expressing RhoA-DN are less affective in retracting filopodia, migrate slower and also form fewer follow-the-leader chain assemblies. Together, these alterations to NC cell intrinsic signaling and cell-cell contact disrupt the precise spatio-temporal post-otic NC cell migratory pattern.     

Closed embryo culture system improved embryological and clinical outcome for single vitrified-warmed blastocyst transfer: A single-center large cohort study

While some studies have shown that the closed embryo culture system (CCS) is a possible improvement over standard embryo culture systems (STS) in terms of early embryonic development, information on clinical outcomes of culturing blastocysts following single vitrified-warmed blastocyst transfer (SVBT) in the CCS and STS remains limited. Therefore, the objective of this single-center, large-cohort, retrospective study was to compare embryonic development until the blastocyst stage and clinical outcomes following SVBT between CCS and STS. From May 2017 to October 2018, 2420 oocytes from 1402 patients who underwent in vitro fertilization and blastocyst culture after minimal stimulation were divided into two groups (CCS and STS). The main outcome measures in the two groups were embryological (blastocyst formation rates and utilized blastocyst rates) and clinical outcomes (ongoing pregnancy rates) after a single vitrified-warmed blastocyst transfer (SVBT). There were no significant differences in the blastocyst formation rates between the CCS and STS groups (59.6% versus 59.1%, p = 0.81). However, there were significant differences in utilized blastocyst rates (51.0% versus 46.6%, p < 0.05). Ongoing pregnancy rates per SVBT cycle were significantly higher in the CCS group than in the STS group (41.4% versus 34.4%, p < 0.05). Moreover, after applying multivariable logistic regression analysis, the type of embryo culture system (CCS to STS, adjusted odds ratios: 1.41, 95% CI: 1.04–1.91) was correlated with ongoing pregnancy. Our study suggests that compared to STS, CCS could improve utilized blastocyst rates and ongoing pregnancy rates to a greater extent, following SVBT.     

<Emphasis Type="Italic">Norrisiella sphaerica</Emphasis> gen. et sp. nov., a new coccoid chlorarachniophyte from Baja California,Mexico

A new chlorarachniophyte, Norrisiella sphaerica S. Ota et K. Ishida gen. et sp. nov., from the coast of Baja California, Mexico is described. We examined its morphology, ultrastructure, and life cycle in detail, using light microscopy, transmission electron microscopy, and time-lapse videomicroscopy. We found that this chlorarachniophyte possessed the following characteristics: (1) vegetative cells were coccoid and possessed a cell wall, (2) a pyrenoid was slightly invaded by plate-like periplastidial compartment from the tip of the pyrenoid, (3) a nucleomorph was located near the pyrenoid base in the periplastidial compartment, (4) cells reproduced vegetatively via autospores, and (5) a flagellate stage was present in the life cycle. This combination of characteristics differs from any of the described chlorarachniophyte genera, and therefore a new genus is established. Fluorescent microscopic observations suggested that the alga formed multinucleate cells prior to forming autospores. Time-lapse observations during autospore formation showed that cytokinesis occurred simultaneously in the multinucleate cells. Zoospores were also produced, and video sequences captured the release of zoospores from coccoid cells. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

英国生物技术产业创新创业生态系统的构建与启示

生物技术产业是各大经济体在21世纪优先发展的战略性产业,逐步成为世界经济的主导产业.英国生物技术产业规模在欧洲排名第一,创新创业文化浓厚.通过孵化器运营案例详细阐述英国生物技术产业发展的生态系统构建.针对我国生物技术产业创新环境提出相应建议,以期对我国生物医药产业的创新创业发展提供借鉴.     

Microtubule-dependent formation of the stigmoid body as a cytoplasmic inclusion distinct from pathological aggresomes

The stigmoid body (STB) is a neurocytoplasmic inclusion containing huntingtin-associated protein 1 (HAP1), an interactor of huntingtin, and its formation is induced by transfection of HAP1-cDNA into cultured cells. Although STB is believed to play a protective role in polyglutamine diseases, including Huntington’s disease and spinal and bulbar muscular atrophy, by sequestering the causative proteins, huntingtin and androgen receptor, respectively, its physiological function and formation remain poorly understood. Therefore, STB is occasionally confused with another cytoplasmic inclusion observed in polyglutamine diseases, the aggresome. Here we examined the subcellular dynamics of STB and compared it immunohistochemically and cytochemically with the aggresome in the rat brain and COS-7 or HeLa cells transfected with HAP1 and/or polyglutamine disease-associated genes. In time-lapse image analysis of HAP1-transfected cells, the HAP1-induced STB is formed from multiple fusions of small HAP1 inclusions characterized by vigorous cytoplasmic movement. In HAP1-transfected cells treated with a microtubule-depolymerizing drug, although the formation of small HAP1 inclusions was not affected, their fusion was critically inhibited. Immunohistochemistry and cytochemistry revealed the absence of association between STB and aggresomal markers, such as ubiquitin/proteasome, intermediate filaments, and the centrosome. Taken together, we concluded that STB is formed by a two-step process comprising microtubule-independent formation of small HAP1 inclusions and microtubule-dependent fusion of these inclusions, and that STB is distinct from pathological aggresomes.