Biology subjects

Straka, J.

Publications and source records attributed to Straka, J..

7 recordsLinked to original sources

bioRxiv2026

Genome-wide CRISPR screens identify DNA repair and R-loop suppression as regulators of the cellular sensitivity to environmentally relevant Bisphenol A exposure

Bisphenol A (BPA) is a prevalent chemical used in the production of plastics. While adverse effects on the reproductive system have been documented, more recent studies also associated BPA exposure with carcinogenesis as well as genomic instability. However, these studies were generally performed using BPA concentrations much higher than those observed in the serum or urine of the general population, making their relevance unclear. To address this, we report here an unbiased genetic study to identify mechanisms responding to environmentally relevant BPA exposure. We performed genome-wide CRISPR knockout screens in HeLa and RPE1 cells upon continuous exposure to 0.5uM BPA, a concentration similar to the mean BPA concentration found in the urine of plastics manufacturing workers, for 19 days. We found genome stability genes among the top common hits between the two cell lines, suggesting that BPA causes DNA damage at this environmentally relevant exposure dose. We validated the DNA repair gene RAD51C and the RNA helicase DDX21 as genes required for BPA resistance. Moreover, we show that BPA exposure increases the formation of R-loops which are resolved by DDX21. Our study suggests that BPA exposure at environmentally relevant doses can cause DNA damage, highlighting the relevance of BPA for carcinogenesis.

genetics↗

bioRxiv2022

Genetic evidence for parthenogenesis in small carpenter bee, Ceratina dallatoreana in its native distribution area

Arrhenotoky is typical mode of reproduction for Hymenoptera - females originate from fertilized eggs, males from unfertilized eggs. However, some lineages of Hymenoptera have switched to thelytoky, where diploid females originate instead from unfertilized diploid eggs. In the contras with some other hymenopteran lineages, thelytoky is generally very rare in bees. Here, we examined reproduction in the small carpenter bee Ceratina dallatoreana, which is assumed to be thelytokous. We compared genotype of microsatellite loci between mothers and their offspring. Offspring were genetically identical with mother in all cases. We did not detect any male offspring. Therefore, we conclude that parthenogeny is the prevailing, and perhaps obligate, mode of reproduction in C. dallatoreana. Offspring were clones of their mother with no observed decrease of heterozygosity. Thus the cytological mode of parthenogenesis is apomixis, or automimic with central fusion and extremely reduced or non-existing recombination. Ceratina bees are originally facultatively eusocial, therefore thelytoky may influence social evolution by causing extremely high within-colony relatedness. However, to date no multifemale nests have been recorded in C. dallatoreana.

genetics↗

bioRxiv2021

Lagging strand gap suppression connects BRCA-mediated fork protection to nucleosome assembly by ensuring PCNA-dependent CAF-1 recycling

The inability to protect stalled replication forks from nucleolytic degradation drives genome instability and is associated with chemosensitivity in BRCA-deficient tumors. An emerging hallmark of BRCA deficiency is the inability to suppress replication-associated single-stranded DNA (ssDNA) gaps. Here, we report that ssDNA gaps on the lagging strand interfere with the ASF1-CAF-1 pathway of nucleosome assembly, and drive fork degradation in BRCA-deficient cells. We show that CAF-1 function at replication forks is lost in BRCA-deficient cells, due to its sequestration at inactive replication factories during replication stress. This CAF-1 recycling defect is caused by the accumulation of Pol-dependent lagging strand gaps, which preclude PCNA unloading, causing sequestration of PCNA-CAF-1 complexes on chromatin. Importantly, correcting PCNA unloading defects in BRCA-deficient cells restores fork stability in a CAF-1-dependent manner. We also show that the activation of a HIRA-dependent compensatory histone deposition pathway restores fork stability to BRCA-deficient cells upon CAF-1 loss. We thus define nucleosome assembly as a critical determinant of BRCA-mediated fork stability. We further reveal lagging strand ssDNA gaps as drivers of fork degradation in BRCA-deficient cells, which operate by inhibiting PCNA unloading and CAF-1-dependent nucleosome assembly.

molecular biology↗

bioRxiv2021

Individual-level specialisation and interspecific resource partitioning in bees revealed by pollen DNA metabarcoding

It is increasingly recognised that intraspecific variation in traits, such as morphology, behaviour, or diet is both ubiquitous and ecologically important. While many species of predators and herbivores are known to display high levels of between-individual diet variation, there is a lack of studies on pollinators. It is important to fill in this gap because individual-level specialisation of flower-visiting insects is expected to affect their efficiency as pollinators with consequences for plant reproduction. Accordingly, the aim of our study was to quantify the level of individual-level specialisation and foraging preferences, as well as interspecific resource partitioning, across different temporal scales in three co-occurring species of bees of the genus Ceratina (Hymenoptera: Apidae: Xylocopinae), C. chalybea, C. nigrolabiata, and C. cucurbitina. We conducted a field experiment where we provided artificial nesting opportunities for the bees and combined a short-term mark-recapture study with the dissection of the bees nests to obtain repeated samples from individual foraging females and complete pollen provisions from their nests. Hence, we could study variation of the composition of pollen collected by the bees at different temporal scales. We used DNA metabarcoding based on the ITS2 locus to identify the composition of the pollen samples. We found that the composition of pollen carried on the bodies of female bees and stored in the brood provisions in their nests significantly differed among the three co-occurring species. At the intraspecific level, individual females consistently differed in their level of specialisation and in the composition of pollen carried on their bodies and stored in their nests. Our study thus provides evidence of consistent individual-level specialisation in pollinators across multiple temporal scales. We also demonstrate that higher generalisation at the species level stemmed from larger among-individual variation in diets as observed in other types of consumers, such as predators. Our study thus reveals how specialisation and foraging preferences of bees change from the scale of individual foraging bouts to complete pollen provisions accumulated in their nests over their lifetime. Such multi-scale view of foraging behaviour is necessary to improve our understanding of the functioning of plant-flower visitor communities.

ecology↗

bioRxiv2021

Are plants in sown flower strips suitable for communities of wild bees? Pollination network approach in conservation biology

O_LIDrastic reductions of insect diversity and abundance are observed in the highly fragmented agricultural landscapes of central Europe. Declines of pollinators may have detrimental effects on the reproduction of wild insect-pollinated plants as well as the yield of crops. In order to mitigate such impacts, sown flower strips on arable land within Agri-Environment Climate Schemes (AECS) are supported across EU countries. However, it is not clear whether sown flower strips provide equivalent benefits to wild flower-visiting insects as semi-natural habitats. C_LIO_LIHere, we apply plant-pollinator network approach to evaluate the function of sown flower strips for the communities of wild bees. We compared the structural characteristics and the robustness of plant-pollinator networks in sown flower strips and nearby semi-natural habitats. We also quantified the importance of individual plant species for bees based on simulations of plant-pollinator extinction cascades. C_LIO_LIWe found that assemblages of plants and pollinators were less diverse in sown flower strips than in semi-natural habitats, more generalized, and more nested. However, we did not find any significant differences in network robustness to plant-pollinator coextinctions. Further, simulations revealed a large variation in the functional importance among plant species from both habitats. C_LIO_LIWe conclude that although the analysis of network robustness suggested that plants in the sown flower strips and semi-natural habitats were functionally equivalent, this masked important differences among the two habitats. From the conservation point of view, semi-natural habitats were superior in supporting a more diverse community of solitary bees and bumblebees. C_LI

ecology↗

bioRxiv2020

Novel BRAF gene fusions in pediatric histiocytic neoplasms define distinct therapeutic responsiveness to RAF paradox breakers

Pediatric histiocytic neoplasms are clonal hematopoietic disorders driven by mutations activating the mitogen-activated protein kinase (MAPK) pathway, such as BRAF-V600E. In non-BRAFV600E cases, we investigated alternative MAPK mutations and found two novel BRAF gene fusions. We investigated the distinct responsiveness of novel BRAF fusions to RAFi therapies and explored the mechanistic basis of such differential responses compared to other BRAF fusions. Two histiocytic patient tumors were analyzed using the CHOP Comprehensive Next-Gen Sequencing Solid Tumor Panel and a targeted RNA-seq panel for 106 fusion partner genes. In the two M- and L-type histiocytic neoplasms assessed, we found novel and rare BRAF gene fusions, MTAP-BRAF and MS4A6A-BRAF, respectively. Both BRAF fusions activated the MAPK/ PI3K pathways and showed homo- and hetero-dimerization with BRAF and the respective N-terminal fusion partner. In contrast to common BRAF fusions, MTAP-BRAF and MS4A6A-BRAF did not respond to PLX8394 due to a lack of disruption of active fusion homo- and hetero-dimers, which was in turn due to the untargeted, stable dimerization mediated by the N-terminal fusion partners. Conversely, we observed robust suppression with LY3009120 that bound fusion dimers and kept them in an inactivate confirmation. MEKi were found to successfully suppress fusion driven signaling and oncogenic phenotypes. Our finding that PLX8394 does not disrupt MTAP-BRAF or MS4A6A-BRAF dimerization due to contribution of N-terminal partners defines a novel paradigm for the distinct mechanisms sought by BRAF fusions in response to RAFi therapy. Overall, this study highlights the unique and differential biology hijacked by BRAF fusions in response to RAFi and further warrants detailed mechanistic classification of BRAF fusions based on their responsiveness to targeted agents.

cancer biology↗

bioRxiv2020

Unrelated males in colonies of facultatively social bee

Colonies of social Hymenoptera are usually groups of closely related females, in which the dominant female(s) is specialized for reproduction and subordinate females care for immature offspring. Kin selection is thought to be the main factor that supports social cohesion. We have discovered a simple society of the bee Ceratina chalybea with an average of 4.68 colony members that cannot be maintained by kin selection alone. These colonies consisted of old reproductive female, young adults and provisioned brood cells. About half of young adults are unrelated to the old female, and almost all of the young adults are male. The old female provisions new brood cells, while continuing to feed young adult offspring. As young adults do not perform demanding or risky activities, they incur little or no cost, but they do benefit from the food they obtain from the old female.

evolutionary biology↗