Whole-animal imaging, gene function, and the Zebrafish Phenome Project

Imaging can potentially make a major contribution to the Zebrafish Phenome Project, which will probe the functions of vertebrate genes through the generation and phenotyping of mutants. Imaging of whole animals at different developmental stages through adulthood will be used to infer biological function. Cell resolutions will be required to identify cellular mechanism and to detect a full range of organ effects. Light-based imaging of live zebrafish embryos is practical only up to ～2 days of development, owing to increasing pigmentation and diminishing tissue lucency with age. The small size of the zebrafish makes possible whole-animal imaging at cell resolutions by histology and micron-scale tomography (microCT). The histological study of larvae is facilitated by the use of arrays, and histology's standard use in the study of human disease enhances its translational value. Synchrotron microCT with X-rays of moderate energy (10-25 keV) is unimpeded by pigmentation or the tissue thicknesses encountered in zebrafish of larval stages and beyond, and is well-suited to detecting phenotypes that may require 3D modeling. The throughput required for this project will require robotic sample preparation and loading, increases in the dimensions and sensitivity of scintillator and CCD chips, increases in computer power, and the development of new approaches to image processing, segmentation, and quantification.     

Findings of somatosensory evoked potential to stimulation of the sciatic nerve in two different rat strains.

No comparative study about somatosensory evoked potentials (SEP) on different rat strains has been done yet. It is evident that comparative SEP studies are important since different rat strains have different physiological properties. We aimed to compare early latency SEP values from stimulation of sciatic nerve in Wistar (Wr) and Sprague-Dawley (SDr) rats which are frequently used rat strains in experimental studies. In Wr group, the mean of first far field potential (Ff1) latency was shorter and the mean Ff1 amplitude was lower than that of Sprague-Dawley rat group. Mean cortical potential latency in Wr group was longer than that of SDr group while amplitude was not different. Central conduction time (CCT) in Wistar rat group was found to be longer than that of SDr group. Shorter Ff1 latency in Wr group implies that afferent volley reaches cervical posterior fasciculus from sciatic nerve earlier than SDr group while longer CP latency implies that afferent volley reaches cortex later than SDr group. Similarity between the latencies of lumbar potentials implies that peripheral conduction velocity has no effect on the difference of Ff1 latencies.     

The untapped potential of the GENSAT mice—A valuable resource for developmental biology

Gene Expression Nervous System Atlas (GENSAT) transgenic mice express EGFP, tdTomato, or Cre recombinase in a wide range of cell types. The mice and the bacterial artificial chromosome transgenes are available from repositories (MMRRC or CHORI), thereby making these resources readily available to the research community. This resource of 1,386 transgenic lines was developed and validated for neuroscience research. However, GENSAT mice have many potential applications in other contexts including studies of development outside of the CNS. The cell type‐specific expression of fluorescent proteins in these mice has been used to identify cells in living embryos, in living embryo explants, and in stem or progenitor cell populations in postnatal tissues. The large number of fluorescent protein driver lines generated by GENSAT greatly expands the range of cell type markers that can be used for live cell sorting. In addition, the GENSAT project has generated 278 new Cre driver lines. This review provides an overview of the GENSAT lines and information for identifying lines that may be useful for a particular application. I also provide a review of the few published cases in which GENSAT mice have been used for studies of embryonic development or analysis of stem/progenitor cells in nonneural tissues. genesis 54:245–256, 2016. © 2016 Wiley Periodicals, Inc.     

Siberian plants: untapped repertoire of bioactive endosymbionts

Background

Endosymbionts are microorganisms present in all plant species, and constitute the subject of interest among the scientific community. These symbionts have gained considerable attention in recent years, owing to their emerging biological roles. Global challenges, such as antimicrobial resistance, treatment of infectious diseases such as HIV and tuberculosis, cancer, and many genetic disorders, exist. Endosymbionts can help address these challenges by secreting valueadded bioactive compounds with various activities.

Objective

Herein, we describe the importance of plants inhabiting Siberian niches. These plants are considered to be among the least studied organisms in the plant kingdom worldwide. Barcoding these plants can be of interest for exploring bioactive endosymbionts possessing myriad biological properties.

Methods

A systematic survey of relevant scientific reports was conducted using the PubMed search engine. The reports were analyzed, and compiled to draft this review.

Results

The literature survey on Siberian plants regarding endosymbionts included a few reports, since extremely few exploratory studies have been conducted on the plants in these regions. Studies on the endosymbionts of these plants are highly valuable, as they report potent endosymbionts possessing numerous biological properties. Based on these considerations, this review aims to create awareness among the global scientific community working on related areas.

Conclusion

This review could provide the basis for barcoding novel endosymbionts of Siberian plants and their ecological importance, which can be exploited in various sectors. The main purpose of this review is to create awareness of Siberian plants, which are among the least studied organisms in the plant kingdom, with respect to endosymbionts, among the scientific community.

     

From the Genome to the Phenome: Tools to Understand the Basic Biology of Plasmodium falciparum

Malaria plagues one out of every 30 humans and contributes to almost a million deaths, and the problem could worsen. Our current therapeutic options are compromised by emerging resistance by the parasite to our front line drugs. It is thus imperative to better understand the basic biology of the parasite and develop novel drugs to stem this disease. The most facile approach to analyse a gene's function is to remove it from the genome or inhibit its activity. Although genetic manipulation of the human malaria parasite Plasmodium falciparum is a relatively standard procedure, there is no optimal method to perturb genes essential to the intraerythrocytic development cycle—the part of the life cycle that produces the clinical manifestation of malaria. This is a severe impediment to progress because the phenotype we wish to study is exactly the one that is so elusive. In the absence of any utilitarian way to conditionally delete essential genes, we are prevented from investigating the parasite's most vulnerable points. This review aims to focus on the development of tools identifying essential genes of P. falciparum and our ability to elicit phenotypic mutation.     

Brugia pahangi: quantitative analysis of infection in several inbred rat strains.

We report a comprehensive study of the infectivity of Brugia pahangi in male and female rats of eight different inbred strains. A single infection of any inbred rat strain will produce rats that become microfilaremic, have occult infection, or clear the primary infection. The proportion belonging to any category is determined by the basic susceptibility level of that strain. Patency rates (blood microfilaria+) ranged from 24% (AO rats) to 73% (WKA rats). The period for which microfilaria were in the circulation was directly related to microfilarial burden, with rats carrying less than 50 mf/ml of blood patent for 11.8 weeks +/- 12.2; for 50-499 mf/ml it was 37.6 +/- 14.8 and for 500+ mf/ml it was 63.3 +/- 34.2 weeks. Suckling rats were resistant to infection (0 patent) and weanlings were intermediate in resistance between suckling and adult rats. Female rats were highly resistant to infection. Approximately half of amicrofilaremic rats have occult infections. A high proportion of patent infections involve the testes or testicular lymphatics. In the most susceptible rat strains, more than 95% of the administered L3 or developing L4 parasites were killed within 28 days. During the course of the first 6 months, the ratio of males to females fell significantly, suggesting a shorter life span in male worms. The features of the infectivity/patency patterns in rats are compared with recognized patterns obtaining in human populations. We conclude that rats provide a valuable and underutilized model for the experimental analysis of filarial infections.     

Modelling the carbon cycle of Miscanthus plantations: existing models and the potential for their improvement

The lignocellulosic perennial grass Miscanthus has received considerable attention as a potential bioenergy crop over the last 25 years, but few commercial plantations exist globally. This is partly due to the uncertainty associated with claims that land‐use change (LUC) to Miscanthus will result in both commercially viable yields and net increases in carbon (C) storage. To simulate what the effects may be after LUC to Miscanthus, six process‐based models have been parameterized for Miscanthus and here we review how these models operate. This review provides an overview of the key Miscanthus soil organic matter models and then highlights what measurers can do to accelerate model development. Each model (WIMOVAC, BioCro, Agro‐IBIS, DAYCENT, DNDC and ECOSSE) is capable of simulating biomass production and soil C dynamics based on specific site characteristics. Understanding the design of these models is important in model selection as well as being important for field researchers to collect the most relevant data to improve model performance. The rapid increase in models parameterized for Miscanthus is promising, but refinements and improvements are still required to ensure that model predictions are reliable and can be applied to spatial scales relevant for policy. Specific improvements, needed to ensure the models are applicable for a range of environmental conditions, come under two categories: (i) increased data generation and (ii) development of frameworks and databases to allow simulations of ranging scales. Research into nonfood bioenergy crops such as Miscanthus is relatively recent and this review highlights that there are still a number of knowledge gaps regarding Miscanthus specifically. For example, the low input requirements of Miscanthus make it particularly attractive as a bioenergy crop, but it is essential that we increase our understanding of the crop's nutrient remobilization and ability to host N‐fixing organisms to derive the most accurate simulations.     

Rat traps: filling the toolbox for manipulating the rat genome

The laboratory rat is rapidly gaining momentum as a mammalian genetic model organism. Although traditional forward genetic approaches are well established, recent technological developments have enabled efficient gene targeting and mutant generation. Here we outline the current status, possibilities and application of these techniques in the rat.     

The Amaryllidaceae alkaloids: an untapped source of acetylcholinesterase inhibitors

Phytochemistry Reviews - The AChE inhibitory activity of alkaloid extracts and compounds has been in the focus of research on the plants of Amaryllidoideae subfamily since the approval of...     

Nanomaterials as a potential environmental pollutant: Overview of existing risk assessment methodologies

The development and use of engineered nanomaterials is increasing rapidly and there are already a large number of consumer products containing nanomaterials. The possible release of nanomaterials from these products is still uncertain, as is their final fate and effects in the environment. Regulators need to deal with this lack of data when carrying out risk assessment and modify the existing risk assessment approaches to adapt them to the unique features of nanomaterials. Here we give an overview of various risk assessment approaches for nanomaterials developed worldwide, in which we describe their strengths and limitations, and have evaluated two of them, the Nano Risk Framework and the Precautionary Matrix for specific cases. Many properties of engineered nanomaterials are unknown and this causes deficiencies in the approaches studied. It is therefore essential to increase the present scarce data on nanomaterials released in the environment and close the gaps in the current methodologies to perform adequate risk assessment for nanomaterials.     

Differences in acute hypoxic pulmonary vasoresponsiveness between rat strains: role of endothelium.

Intact Madison (M) rats have greater pulmonary pressor responses to acute hypoxia than Hilltop (H) rats. We tested the hypothesis that the difference in pressor response is intrinsic to pulmonary arteries and that endothelium contributes to the difference. Pulmonary arteries precontracted with phenylephrine (10(-7) M) from M rats had greater constrictor responses [hypoxic pulmonary vasoconstriction (HPV)] to acute hypoxia (0% O(2)) than those from H rats: 473 +/- 30 vs. 394 +/- 29 mg (P < 0.05). Removal of the endothelium or inhibition of nitric oxide (NO) synthase by N(omega)-nitro-L-arginine (L-NA, 10(-3) M) significantly blunted HPV in both strains. Inhibition of cyclooxygenase by meclofenamate (10(-5) M) or blockade of endothelin type A and B receptors by BQ-610 (10(-5) M) + BQ-788 (10(-5) M), respectively, had no effect on HPV. Constrictor responses to phenylephrine, endothelin-1, and prostaglandin F(2alpha) were similar in pulmonary arteries from both strains. The relaxation response to ACh, an NO synthase stimulator, was significantly greater in M than in H rats (80 +/- 3 vs. 62 +/- 4%, P < 0.01), but there was no difference in response to sodium nitroprusside, an NO donor. L-NA potentiated phenylephrine-induced contraction to a greater extent in pulmonary arteries from M than from H rats. These findings indicate that at least part of the strain-related difference in acute HPV is attributable to differences in endothelial function, possibly related to differences in NO production.     

Action potential conduction velocity along the caudal and tibial nerves in rat strains selected for excitability of the neuromuscular system

The study was performed on 2 lines of rat selected for high (H) and low (L) excitability threshold of the nervous-muscle apparatus. H-line rats have higher values of spike conduction velocity in caudal and tibial nerves, as compared to those obtained in L-line rats. It is suggested that behavioral differences between these two lines of rat may be connected with changes of neurological characters both of peripheral and central nervous system, as a result of selection.