Explore the vast range of titles available.

The mechanisms for human germ cell development have remained largely unknown, due to the difficulty in obtaining suitable experimental materials. The establishment of an in vitro system to reconstitute human germ cell development will thus provide a critical opportunity to understand its mechanisms at a molecular level. It has previously been shown that human induced pluripotent stem cells (hiPSCs) are first induced into incipient mesoderm-like cells (iMeLCs), which are in turn induced into primordial germ-cell like cells (PGCLCs) with gene expression properties similar to early migratory PGCs. Here, we report that the efficiency of PGCLC induction varies among hiPSC clones, and, interestingly, the clonal variations in PGCLC induction efficiency are reflected in the gene expression states of the iMeLCs. Remarkably, the expression levels of EOMES, MIXL1, or T in the iMeLCs are positively correlated with the efficiency of subsequent PGCLC generation, while the expressions of CDH1, SOX3, or FGF2 are negatively correlated. These results indicate that the expression changes of these genes occurring during iMeLC induction are key markers indicative of successful induction of PGCLCs, and furthermore, that hiPSC clones have different properties that influence their responsivity to the iMeLC induction. Our study thus provides important insights into the mechanism of hPGC specification as well as the development of a better strategy for inducing human germ cell fate from PSCs in vitro. Summary Sentence Gene expression responses to activin A/WNT signaling vary among clones of human induced pluripotent stem cells, and these differences greatly reflect the clonal variations in the induction efficiency into in vitro primordial germ cells.

Mammalian expression platforms are primary production systems for therapeutic proteins that require complex post-translational modifications. Current processes used for developing recombinant mammalian cell lines generate clonal cell lines with high phenotypic heterogeneity, which has puzzled researchers that use mammalian cell culture systems for a long time. Advances in mammalian genome-editing technologies and systems biotechnology have shed light on clonal variation and enabled rational cell engineering in a targeted manner. We propose a new approach for a next-generation cell line development platform that can minimize clonal variation. Combined with the knowledge-based selection of ideal integration sites and engineering targets, targeted integration-based cell line development will allow tailored control of recombinant gene expression with predicted phenotypes. Recombinant mammalian cell line development is a critical step in the current manufacturing process for large-scale production of therapeutic proteins. The current process of cell line development using random transgene integration induces high phenotypic heterogeneity among recombinant clones, thus limiting predictive value, process streamlining, and cost-effectiveness in biopharmaceutical drug discovery and development. Recent advances in genome-editing technologies and systems biology approaches offer new insight into cell line development to minimize clonal variation. Targeted engineering strategies, combined with engineering target/integration site discovery based on multiomics data sets and in silico models, have the potential to streamline the process of cell line development with highly predictable gene expression among recombinant clones.

Genetic variation between individuals has been extensively investigated, but differences between tissues within individuals are far less understood. It is commonly assumed that all healthy cells that arise from the same zygote possess the same genomic content, with a few known exceptions in the immune system and germ line. However, a growing body of evidence shows that genomic variation exists between differentiated tissues. We investigated the scope of somatic genomic variation between tissues within humans. Analysis of copy number variation by high-resolution array-comparative genomic hybridization in diverse tissues from six unrelated subjects reveals a significant number of intraindividual genomic changes between tissues. Many (79%) of these events affect genes. Our results have important consequences for understanding normal genetic and phenotypic variation within individuals, and they have significant implications for both the etiology of genetic diseases such as cancer and for immortalized cell lines that might be used in research and therapeutics.

BackgroundClonal plants spread laterally by spacers between their ramets (shoot–root units); these spacers can transport and store resources. While much is known about how clonality promotes plant fitness, we know little about how different clonal plants influence ecosystem functions related to carbon, nutrient and water cycling.ApproachThe response–effect trait framework is used to formulate hypotheses about the impact of clonality on ecosystems. Central to this framework is the degree of correspondence between interspecific variation in clonal ‘response traits’ that promote plant fitness and interspecific variation in ‘effect traits’, which define a plant's potential effect on ecosystem functions. The main example presented to illustrate this concept concerns clonal traits of vascular plant species that determine their lateral extension patterns. In combination with the different degrees of decomposability of litter derived from their spacers, leaves, roots and stems, these clonal traits should determine associated spatial and temporal patterns in soil organic matter accumulation, nutrient availability and water retention.ConclusionsThis review gives some concrete pointers as to how to implement this new research agenda through a combination of (1) standardized screening of predominant species in ecosystems for clonal response traits and for effect traits related to carbon, nutrient and water cycling; (2) analysing the overlap between variation in these response traits and effect traits across species; (3) linking spatial and temporal patterns of clonal species in the field to those for soil properties related to carbon, nutrient and water stocks and dynamics; and (4) studying the effects of biotic interactions and feedbacks between resource heterogeneity and clonality. Linking these to environmental changes may help us to better understand and predict the role of clonal plants in modulating impacts of climate change and human activities on ecosystem functions.

Defense mechanisms were studied for Pinus brutia, a cornerstone Turkish forest tree, against pine processionary moth damage by Thaumetopoea pityocampa (Den. & Schiff.) and Thaumetopoea wilkinsoni Tams 1926 moth species. This research addressed the significance of Pinus brutia in afforestation and breeding. The expression of enzymatic antioxidants (SOD, POD, CAT, APX) and photosynthetic pigments (chlorophylls and carotenoids) at a clonal level in response to insect damage was assessed. Approximately 84 needle samples from 28 Pinus brutia clones from the Antalya Düzlerçamı Brutian Pine Seed Orchard were studied. Samples were collected in February and August 2021 to capture responses during key insect activity periods. These samples were then analyzed for pigment concentrations and antioxidant activities. Statistical analysis revealed that sampling period and clone significantly affected chlorophyll and carotenoid levels. The POD and SOD activities were primarily influenced by the sampling period. However, CAT activity was affected by the number of insect pouches, the period, and the clone. APX activity was significantly impacted by both pouch number and sampling period. These findings offer insights into how seasonal changes and genetic variations modulate P. brutia clones’ defense mechanisms against pine processionary moth infestations, informing future forest management.

Background Fruit set is the transformation of flower ovaries into berries. Fruit set rate determines the number of berries produced per bunch, which is a major component of yield in grapevines. Malbec is a black-berried grapevine cultivar recognized for producing high-quality wines, and particularly relevant for Argentina’s winemaking industry. Clonal variation has been reported for Malbec at the phenotypic and molecular levels. However, less is known about clonal variation for agronomically relevant features affecting yield. In this work we evaluated 25 Malbec clones for the fruit set rate and other related features over multiple seasons. Results The mean fruit set rate was 38.6% (ranged between 13.1% and 65.8%) in 2021/22, and 32.1% (ranged between 9.8% and 50%) in 2022/23 season, evidencing a wide range of within-season variation. Besides the expectable interannual differences, significant and positive correlations were found over seasons for the fruit set rate, number of flowers per inflorescence and number of berries per bunch. Moreover, multivariate clustering analyses consistently grouped the evaluated clones into three distinct groups. Two of these groups showed similar number of flowers per inflorescence, but significantly different fruit set rates and number of berries per bunch. Representative clones of the latter two groups were in-depth analyzed in 2023/24, supporting previous seasons results and revealing differences in their floral phenotypes. Conclusions We found a wide range of clone-dependent variation for the evaluated traits, which generated great differences in the reproductive performance and yield within Malbec. We hypothesized that the observed differences were associated to somatic mutations, affecting the correct development and functionality of flower organs in a clone-specific way.

Seed orchards with high hereditary qualities and the improvement studies used are of great importance. This study was carried out on individuals in a Boyabat grafted black pine seed orchard, Sinop. The morphological and micromorphological measurements of the characteristics were performed on needle samples taken from individuals, and the genetic diversity was determined on a clonal basis. According to the analysis of variance applied to the data obtained from the measurements and the morphological and micromorphological characters of the clones, it was determined that there was a significant difference among the clones at the P<0.001 confidence level.  In this context, according to Duncan’s Range test, the creation of a large number of groups is an indicator of it. The highest heritability rates were obtained in needle diameter, stipule diameter, number of the dorsal stoma, and needle length characteristics.

Abstract Long-lived plants face the challenge of ever-increasing mutational burden across their long lifespan. Early sequestration of meristematic stem cells is supposed to efficiently slow down this process, but direct measurement of somatic mutations that accompanies segregated cell lineages in plants is still rare. Here, we tracked somatic mutations in 33 leaves and 22 adventitious roots from 22 stem-cuttings across eight major branches of a shrub willow (Salix suchowensis). We found that most mutations propagated separately in leaves and roots, providing clear evidence for early segregation of underlying cell lineages. By combining lineage tracking with allele frequency analysis, our results revealed a set of mutations shared by distinct branches, but were exclusively present in leaves and not in roots. These mutations were likely propagated by rapidly dividing somatic cell lineages which survive several iterations of branching, distinct from the slowly dividing axillary stem cell lineages. Leaf is thus contributed by both slowly and rapidly dividing cell lineages, leading to varied fixation chances of propagated mutations. By contrast, each root likely arises from a single founder cell within the adventitious stem cell lineages. Our findings give straightforward evidence that early segregation of meristems slows down mutation accumulation in axillary meristems, implying a plant “germline” paralog to the germline of animals through convergent evolution.

Background Epigenetic modifications, such as DNA methylation, regulate transcription and influence key biological traits. While many efforts were made to understand their stability in annual crops, their long-term persistence in clonally propagated plants remains poorly understood. Grapevine ( Vitis vinifera ) provides a unique model, with cultivars vegetatively propagated for centuries. Results Here, we assemble the phased genomes of Cabernet Sauvignon and its parental lineages, Cabernet Franc and Sauvignon Blanc, using HiFi long-reads and a gene map tenfold denser than existing maps. Using three clones per cultivar, we quantify methylation with very consistent short- and long-read sequencing and ensure both varietal representativeness and assessment of clonal variability. We leverage the parent-progeny sequence graph to highlight allele-specific methylation and conserved transcriptomic patterns for genes and small RNA. Such a format is essential to integrate multi-omics data and reveals that, despite less clonal conservation than genetic polymorphisms, methylation marks are remarkably inherited. By further demonstrating the linear-reference limitations, we determine that the correct representation of genetic variants by the sequence graph is crucial for the accurate allelic quantification of the methylome. Conclusions These findings reveal the remarkable stability of epigenetic marks in a model propagated by asexual reproduction. Using a phased sequence graph, we introduce a scalable framework that accounts for genomic variation, accurately quantifies allele-specific methylation, and supports multi-omics integration such as our evaluation of the transcriptional impact of epigenetic inheritance. This approach has broad implications for perennial crops, where epigenetic variation could influence traits relevant to breeding, adaptation, and long-term agricultural sustainability.

It is important to evenly increase the amount of scattered pollen per clone for maintaining high genetic variation in clonal seed orchards. It is thus imperative to determine not only the number of male flowers per tree, but also the amount of pollen per male flower in each clone. In this study, the existence of annual variation on the fresh weight of male flowers (FW) and the clonal and annual variation, and ramets’ variation with the same or different tree ages on the weight of pollen per male flower (WP) were investigated using 21 clones for 3 years. The results indicated that there were significant differences in FW and WP among clones each year and the relationships between FW and WP were linearly significant for every year. WP also showed significant annual variation, while the re was also significant variation in ramets. The clonal repeatability regarding WP was 0.37—0.47 for data obtained for 2 or 3 years and the generalized linear mixed models with the random effects of clone, year, and ramet indicated that the effect of clone more strongly affected WP than other effects. These results suggested that WP on is a trait that is considerably influenced by clonal characteristics; there is thus a need to characterize this trait in each clone when using seed orchards.