bulk-segregant analysis Dotaz Zobrazit nápovědu
The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes.
UNLABELLED: Transmission of genetic material from one generation to the next is a fundamental feature of all living cells. In eukaryotes, a macromolecular complex called the kinetochore plays crucial roles during chromosome segregation by linking chromosomes to spindle microtubules. Little is known about this process in evolutionarily diverse protists. Within the supergroup Discoba, Euglenozoa forms a speciose group of unicellular flagellates-kinetoplastids, euglenids, and diplonemids. Kinetoplastids have an unconventional kinetochore system, while euglenids have subunits that are conserved among most eukaryotes. For diplonemids, a group of extremely diverse and abundant marine flagellates, it remains unclear what kind of kinetochores are present. Here, we employed deep homology detection protocols using profile-versus-profile Hidden Markov Model searches and AlphaFold-based structural comparisons to detect homologies that might have been previously missed. Interestingly, we still could not detect orthologs for most of the kinetoplastid or canonical kinetochore subunits with few exceptions including a putative centromere-specific histone H3 variant (cenH3/CENP-A), the spindle checkpoint protein Mad2, the chromosomal passenger complex members Aurora and INCENP, and broadly conserved proteins like CLK kinase and the meiotic synaptonemal complex proteins SYCP2/3 that also function at kinetoplastid kinetochores. We examined the localization of five candidate kinetochore-associated proteins in the model diplonemid, Paradiplonema papillatum. PpCENP-A shows discrete dots in the nucleus, implying that it is likely a kinetochore component. PpMad2, PpCLKKKT10/19, PpSYCP2L1KKT17/18, and PpINCENP reside in the nucleus, but no clear kinetochore localization was observed. Altogether, these results point to the possibility that diplonemids evolved a hitherto unknown type of kinetochore system. IMPORTANCE: A macromolecular assembly called the kinetochore is essential for the segregation of genetic material during eukaryotic cell division. Therefore, characterization of kinetochores across species is essential for understanding the mechanisms involved in this key process across the eukaryotic tree of life. In particular, little is known about kinetochores in divergent protists such as Euglenozoa, a group of unicellular flagellates that includes kinetoplastids, euglenids, and diplonemids, the latter being a highly diverse and abundant component of marine plankton. While kinetoplastids have an unconventional kinetochore system and euglenids have a canonical one similar to traditional model eukaryotes, preliminary searches detected neither unconventional nor canonical kinetochore components in diplonemids. Here, we employed state-of-the-art deep homology detection protocols but still could not detect orthologs for the bulk of kinetoplastid-specific nor canonical kinetochore proteins in diplonemids except for a putative centromere-specific histone H3 variant. Our results suggest that diplonemids evolved kinetochores that do not resemble previously known ones.
High concentrations of airborne asbestos in the ambient air are still a serious problem of air quality in numerous localities around the world. Since 2002, elevated concentrations of asbestos minerals of unknown origin have been detected in the ambient air of Pilsen, Czech Republic. To determine the asbestos fibre sources in this urban air, a systematic study was conducted. First, 14 bulk dust samples were collected in Pilsen at nine localities, and 6 bulk samples of construction aggregates for gravel production were collected in a quarry in the Pilsen-Litice district. The quarry is the largest quarry in the Pilsen region and the closest quarry to the built-up urban area. X-ray diffraction of the asbestos minerals revealed that monoclinic amphibole (MA, namely actinolite based on subsequent SEM-EDX analysis) in the bulk samples accounted for < 1-33% of the mass and that the highest values were found in the bulk dust samples from the railway platform of the Pilsen main railway station. Simultaneously, 24-h samples of airborne particulate matter (PM) at three localities in Pilsen were collected. Actinolite was identified in 40% of the PM samples. The relationship between the meteorology and presence of actinolite in the 24 PM10 samples was not proven, probably due to the long sampling integration time. Therefore, highly time-and-size-resolved PM sampling was performed. Second, sampling of size-segregated aerosols and measurements of the wind speed (WS), wind direction (WD), precipitation (P) and hourly PM10, PM2.5 and PM1 were conducted in a suburban locality near the quarry in two monthly highly time-resolved periods (30, 60, 120 min). Three/eight PM size fractions were sampled by a Davis Rotating-drum Uniform-size-cut Monitor (3/8DRUM) and analysed for the presences of asbestos fibres by scanning electron microscopy with energy dispersive x-ray spectroscopy (SEM-EDX). Asbestos fibre detection in highly time-resolved PM samples and current WD and WS determination allows the apportionment directionality of asbestos fibre sources. The number of critical actinolite asbestos fibres (length ≥ 5 μm and width < 3 μm, 3:1) increased with the PM1-10/PM10 and PM2.5-10/PM10 ratios, WS > 2 m s-1 and precipitation < 1 mm. Additionally, the number of critical actinolite asbestos fibres was not related to a specific WD. Therefore, we conclude that the sources of airborne critical actinolite asbestos fibres in Pilsen's urban area are omnipresent. Frequent use of construction aggregates and gravel from the metamorphic spilite quarries in the Pilsen region and in many localities around the urban area is a plausible explanation for the omnipresence of the critical actinolite asbestos fibres concentration in Pilsen's ambient air. Mitigation strategies to reduce the concentrations of critical actinolite asbestos fibres must be developed. Continuous monitoring and performing SEM-EDX analysis of highly time-and-size-resolved PM samples, correlated with fast changing WS and WD, seems to be a strong tool for efficiently controlling the mitigation strategies of critical actinolite asbestos fibres.
- MeSH
- aerosoly analýza MeSH
- azbest chemie MeSH
- látky znečišťující vzduch analýza MeSH
- mikroskopie elektronová rastrovací MeSH
- monitorování životního prostředí metody MeSH
- pevné částice chemie MeSH
- prach analýza MeSH
- velikost částic MeSH
- znečištění ovzduší MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
