Biology subjects

Farsi, M.

Publications and source records attributed to Farsi, M..

3 recordsLinked to original sources

bioRxiv2025

A method for creating custom 3D-printed molds to facilitate zebrafish imaging studies, including of cardiac development.

Embryo mounting is one of the technical challenges researchers encounter when undertaking an imaging project. Embryos need to be oriented in a reproducible manner such that the tissue of interest is accessible to a microscope objective for the entire imaging period. To overcome this challenge researchers can embed embryos in viscous media or create specialized dishes and casts to hold embryos in a desired orientation during imaging. Here we describe a method for using a cheap stereolithographic (SLA) 3D-printer to manufacture re-usable molds that create agarose wells in which embryos can be mounted for imaging. These agarose wells provide a reliable means for orienting multiple embryos for imaging. This method includes a design framework that can be easily customized for a variety of tissues, organisms and imaging challenges. Using this method we have created molds for imaging cardiac development in zebrafish for both upright and inverted microscopes. By utilizing materials and equipment that are accessible this method allows researchers to easily create molds specific to their mounting needs. SUMMARYHere we describe a method that uses a cheap stereolithographic (SLA) 3D printer to create molds to facilitate the reproducible mounting of zebrafish embryos for imaging studies. Using this method, weve created molds for imaging cardiac morphogenesis in zebrafish embryos.

developmental biology↗

bioRxiv2022

First assessment of Iranian pomegranate germplasm using targeted metabolites and morphological traits to develop the core collection and modeling of the current and future spatial distribution under climate change conditions

Pomegranate has been considered a medicinal plant due to its rich nutrients and bioactive compounds. Since environmental conditions affect the amount and composition of metabolites, selecting suitable locations for cultivation would be vital to achieve optimal production. In this study, the diversity of targeted metabolites and morphological traits among 152 Iranian pomegranate genotypes was evaluated to establish a core collection. The multivariate analyses were conducted including principal component analysis (PCA), and cluster analysis. In addition, the current and future geographical distribution of pomegranate in Iran was predicted to identify suitable locations using the MaxEnt model. The results showed high diversity in the studied morphological and metabolic traits. The PCA results indicated that FFS, NFT, JA, and AA are the most important traits in discriminating the studied genotypes. A constructed core collection using maximization strategy consisted of 20 genotypes and accounted for 13.16% of the entire collection. Shannon-Weaver diversity index of a core collection was similar or greater than the entire collection. Evaluation of the core collection using four parameters of MD, VD, CR, and VR also indicated the maintenance of the genetic diversity of the original set. According to the MaxEnt model, altitude, average temperature of coldest quarter, and isothertmality were the key factors for the distribution of pomegranate. The most suitable areas for pomegranate cultivation were also determined which were located in arid and semi-arid regions of Iran. The geographic distribution of pomegranate in the future showed that the main provinces of pomegranate cultivation would be less affected by climatic conditions by the middle of the century. The results of this study provide valuable information for selection of elite genotypes to develop the breeding programs to obtain the cultivars with the highest levels of metabolic compounds for pharmaceutical purposes, as well as identification of the most suitable agro-ecological zones for orchard establishment.

plant biology↗

bioRxiv2020

Application of DNA barcodes and spatial analysis in conservation genetics and modeling of Iranian Salicornia genetic resources

Iran is one of the origins of some Salicornia species. Nevertheless, so far, comprehensive research has not been conducted on genetic potential, distribution, selection of populations, and the economic utilization of Salicornia in Iran. In the current study, Salicornia was collected based on the previous research locations available on 26 different geographical locations of provinces in Iran. Subsequently, an accurate model was provided for identifying of Salicornia species biodiversity by performing spatial analysis and modeling of distributed areas. The results provided valuable information on the diversity of specific geographical regions, conservation status of existing species, prioritization of conservation areas, and selection of areas for Agro-Ecological, leading to the development of industrial agriculture. Further, we validated genes in the field of DNA barcoding in Salicornia plants using matK, rbcL, trnH-psbA, ycf and ITS2 identifying species groups. Together, integrating our results will provide useful information for the management and utilization of Salicornia genetic resources in Iran.

ecology↗