Somatic embryogenesis in mature zygotic embryos of Picea pungens

This study developed somatic embryogenesis protocols for Picea pungens (Engelm), an important ornamental species, including initiation, proliferation, maturation, germination, and acclimation. Somatic embryogenic tissues were induced from mature zygotic embryos of five families, with a frequency of $$\ge $$ ≥ 22% for each. Embryogenic tissues (ET) from 13 clones of three families were proliferated for one week, achieving an average rate of 179.1%. The ET of 38 clones of three families were cultured in maturation medium for six weeks; 188 mature embryos on average were counted per gram ET cultured, of which $$\ge $$ ≥ 81.1% appeared normal, and each clone developed at least 28 normally matured embryos. A total of 69.9% or more of cotyledonary somatic embryos germinated normally and developed into normal emblings. The experiment of transplanting the emblings into a greenhouse had an average survival rate of 68.5%. Considerable variation among and within families during initiation and proliferation was observed, but this variation decreased in the maturation and germination. Changing the concentration of plant growth regulator of the initiation medium did not significantly change the initiation frequency. We recommend incorporating these protocols into the current Picea pungens practical programs, although further research is essential to increase efficiencies and reduce cost.

Ensemble Learning Approach for the Prediction of Quantitative Rock Damage Using Various Acoustic Emission Parameters

Monitoring rock damage subjected to cracks is an important stage in underground spaces such as radioactive waste disposal repository, civil tunnel, and mining industries. Acoustic emission (AE) technique is one of the methods for monitoring rock damage and has been used by many researchers. To increase the accuracy of the evaluation and prediction of rock damage, it is required to consider various AE parameters, but this work is a difficult problem due to the complexity of the relationship between several AE parameters and rock damage. The purpose of this study is to propose a machine learning (ML)-based prediction model of the quantitative rock damage taking into account of combined features between several AE parameters. To achieve the goal, 10 granite samples from KAERI (Korea Atomic Energy Research Institute) in Daejeon were prepared, and a uniaxial compression test was conducted. To construct a model, random forest (RF) was employed and compared with support vector regression (SVR). The result showed that the generalization performance of RF is higher than that of SVRRBF. The R2, RMSE, and MAPE of the RF for testing data are 0.989, 0.032, and 0.014, respectively, which are acceptable results for application in laboratory scale. As a complementary work, parameter analysis was conducted by means of the Shapley additive explanations (SHAP) for model interpretability. It was confirmed that the cumulative absolute energy and initiation frequency were selected as the main parameter in both high and low-level degrees of the damage. This study suggests the possibility of extension to in-situ application, as subsequent research. Additionally, it provides information that the RF algorithm is a suitable technique and which parameters should be considered for predicting the degree of damage. In future work, we will extend the research to the engineering scale and consider the attenuation characteristics of rocks for practical application.

Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription

ABSTRACTNucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA Polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA, and a divergent non-coding (DNC) transcript with an unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. We identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC in high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements. Nascent transcription profiling showed a genome-wide role of Hda1C in DNC repression. Live-cell imaging of transcription revealed that Hda1C reduced the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC regions, supporting DNC repression by histone deacetylation. Our data support the interpretation that DNC results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.

Breast cancer: Emerging principles of metastasis, adjuvant and neoadjuvant treatment from cancer registry data

BackgroundA growing primary breast cancer (PT) can initiate local (LR), regional (pLN), and distant metastases (MET). Characteristics of these progressions such as initiation, frequency and duration of PT and MET growth describe principles of the MET process. They are bottlenecks through which molecular hypotheses and scientific terms for prediction and prognosis have to go.MethodsPopulation-based data from the Munich Cancer Registry over 4 time periods since 1978 with the most important prognostic factors and a follow-up up to this day are analyzed. With n= 66.818 patients, reliable data are obtained on initiation on METs, growth times und survival even in small subgroups. Together with results of clinical trials on prevention and adjuvant treatment (AT) principles of tumor growth, MET process and AT are summarized.ResultsThe median growth periods for PT/ MET/LR/pLN result in 12,5/8,8/5/3,5 years. Even if 30% of METs only appear after 10 years of MET-free time, a delayed initiation or cascade like initiation of METs, e.g. from pLNs cannot be derived from the data. That is an immediate MET initiation principle by PT. The growth rate of the PT can vary by a factor of 10 or more and can be transferred to the MET. The coupling of the growth rates of PT/MET results in the principle of a nearly constant relation of about 1.4. Principles of AT are the 50% eradication of 1st and 2ndPT, the selective and partial eradication of bone and lung METs with successful ATs, which cannot be improved by extending the duration of ATs. These principles reveal that there is no convincing rationale for the currently accepted early risk of breast cancer by hormone replacement therapies, for long term endocrine ATs or cascade like initiation of METs.ConclusionA paradigm with nine principles for the MET process and ATs can be derived from real world data and clinical trials. The principles suggest alternative interpretations of well-known clinical trials and changes in treatments. The outlined MET process should be generalizable to all solid tumors.

Physiological and Structural Aspects of In Vitro Somatic Embryogenesis in Abies alba Mill

Initiation of somatic embryogenesis from immature zygotic embryos, long-term maintenance of embryogenic tissue in vitro or by cryopreservation, as well as maturation, of somatic embryos of Abies alba Mill. are reported in this study. For the initiation of embryogenic tissues, a DCR medium containing different types of cytokinins (1 mg.L−1) were tested. During three consecutive years, 61 cell lines were initiated out of 1308 explants, with initiation frequencies ranging between 0.83 and 13.33%. The type of cytokinin had no profound effect on the initiation frequency within one given year. Microscopic observations revealed presence of bipolar somatic embryos in all initiated embryogenic tissues. Besides the typical bipolar somatic embryos, huge polyembryonal complexes, as well as “twin” embryos, were observed. Maturation of somatic embryos occurred on a DCR medium supplemented by abscisic acid (10 mg.L−1), polyethylene glycol (PEG-4000, 7.5%) and 3% maltose. The maturation capacity was cell-line dependent. All of the four tested cell lines produced cotyledonary somatic embryos, though at different quantities, of 16 to 252 per g of fresh weight. After germination, seedlings developed, but their further growth soon stopped after the formation of a resting bud. Altogether, seven cell lines were cryopreserved, using the slow-freezing technique. After rewarming, all tested cell lines showed regrowth rates between 81.8 and 100%.

Predictive design of sigma factor-specific promoters

To engineer synthetic gene circuits, molecular building blocks are developed which can modulate gene expression without interference, mutually or with the host’s cell machinery. As the complexity of gene circuits increases, automated design tools and tailored building blocks to ensure perfect tuning of all components in the network are required. Despite the efforts to develop prediction tools that allow forward engineering of promoter transcription initiation frequency (TIF), such a tool is still lacking. Here, we use promoter libraries of E. coli sigma factor 70 (σ70)- and B. subtilis σB-, σF- and σW-dependent promoters to construct prediction models, capable of both predicting promoter TIF and orthogonality of the σ-specific promoters. This is achieved by training a convolutional neural network with high-throughput DNA sequencing data from fluorescence-activated cell sorted promoter libraries. This model functions as the base of the online promoter design tool (ProD), providing tailored promoters for tailored genetic systems.

Dynamics of replication origin over-activation

We determined replication patterns in cancer cells in which the controls that normally prevent excess replication were disrupted (“re-replicating cells”). Single-fiber analyses suggested that replication origins were activated at a higher frequency in re-replicating cells. However, nascent strand sequencing demonstrated that re-replicating cells utilized the same pool of potential replication origins as normally replicating cells. Surprisingly, re-replicating cells exhibited a skewed initiation frequency correlating with replication timing. These patterns differed from the replication profiles observed in non-re-replicating cells exposed to replication stress, which activated a novel group of dormant origins not typically activated during normal mitotic growth. Hence, disruption of the molecular interactions that regulates origin initiation can activate two distinct pools of potential replication origins: re-replicating cells over-activate flexible origins while replication stress in normal mitotic growth activates dormant origins.

Blue sky’s the limit? Somatic embryogenesis as a means of propagating recalcitrant blue spruce (Picea pungens) cultivar Hoopsii

The ‘triple-blue’ cultivar of blue spruce (Picea pungens Hoopsii) is notably recalcitrant towards the realm of traditional vegetative propagation methods. Its ability to naturally proliferate is limited by ovule and embryo abortion during the growing season, leading to low viable seed yield. In this study, we established a protocol using somatic embryogenesis (SE) as a means of propagating this popular ornamental cultivar. We collected cones from Hoopsii trees at seven different timepoints throughout the growing season (mid-June to late July in Ottawa (Plant Hardiness Zone 5A)). Female megagametophytes were harvested following each collection and immature zygotic embryos were plated onto induction media. Early somatic embryos began developing from the embryonic tissue (ET) three to five weeks following induction. The highest ET initiation frequency occurred from embryos collected June 20–July 10, suggesting that developmental stage of the embryo was a significant factor in SE induction. The conversion of mature somatic embryos into plantlets (emblings) was completed in eight–ten weeks at a rate of 92.8%. In this study, we demonstrate that in vitro somatic embryogenesis using our optimized protocol is a fast and prolific method for the mass propagation of Hoopsii blue spruce. This is the first report on the production of somatic Hoopsii emblings.