Building a bi-directional promoter binary vector from the intergenic region of Arabidopsis thaliana cab1 and cab2 divergent genes useful for plant transformation

The ability to express genes in a controlled and limited domain is essential to succeed in targeted genetic modification. Having tools by which to rapidly and conveniently generate constructs which can be assayed in a diverse array of plant species expedites research and end-product development. Targeting specifically green plant tissues offers an opportunity to effect changes to diverse processes such as water use efficiency, photosynthesis, predation and nutrition. To facilitate the generation of transgenes to be expressed in this domain, we created a series of plasmids called p2CABA based on the Arabidopsis thaliana chlorophyll a/b gene promoter, a single natural bidirectional promoter that can drive and express two different genes at the same time. Studies we carried out showed reporter gene, GUS expressed in leaves and stems but not in the roots, as expected since this endogenous promoter controls the expression of two photosynthetic genes in A. thaliana. We, therefore, utilized the intergenic region between the A. thaliana cab1 and cab2 divergent genes to design and construct a bidirectional promoter vector containing two multiple cloning sites and a gateway recombination cassette. This in turn will help minimize gene silencing and achieve desirable expression pattern of transgenes, a critical issue in plant genetic engineering and in this report we show their use in Medicago and tomato.Key words: Arabidopsis cab genes, bidirectional promoters, gene expression, plant genetic engineering, reporter genes, photosynthetic genes

KNOX1 genes regulate lignin deposition and composition in monocots and dicots

Plant secondary cell walls are deposited mostly in vascular tissues such as xylem vessels, tracheids, and fibers. These cell walls are composed of a complex matrix of compounds including cellulose, hemicellulose, and lignin. Lignin functions primarily to maintain the structural and mechanical integrity of both the transport vessel and the entire plant itself. Since lignin has been identified as a major source of biomass for biofuels, regulation of secondary cell wall biosynthesis has been a topic of much recent investigation. Biosynthesis and patterning of lignin involves many developmental and environmental cues including evolutionarily conserved transcriptional regulatory modules and hormonal signals. Here, we investigate the role of the class I Knotted1-like-homeobox (KNOX) genes and gibberellic acid in the lignin biosynthetic pathway in a representative monocot and a representative eudicot. Knotted1 overexpressing mutant plants showed a reduction in lignin content in both maize and tobacco. Expression of four key lignin biosynthesis genes was analyzed and revealed that KNOX1 genes regulate at least two steps in the lignin biosynthesis pathway. The negative regulation of lignin both in a monocot and a eudicot by the maize Kn1 gene suggests that lignin biosynthesis may be preserved across large phylogenetic distances. The evolutionary implications of regulation of lignification across divergent species are discussed

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries

Type Ia Supernova Nucleosynthesis: Metallicity-dependent Yields

Type Ia supernova explosions (SN Ia) are fundamental sources of elements for the chemical evolution of galaxies. They efficiently produce intermediate-mass (with Z between 11 and 20) and iron group elements - for example, about 70% of the solar iron is expected to be made by SN Ia. In this work, we calculate complete abundance yields for 39 models of SN Ia explosions, based on three progenitors - a 1.4 M ⊙ deflagration detonation model, a 1.0 M ⊙ double detonation model, and a 0.8 M ⊙ double detonation model - and 13 metallicities, with 22Ne mass fractions of 0, 1 × 10-7, 1 × 10-6, 1 × 10-5, 1 × 10-4, 1 × 10-3, 2 × 10-3, 5 × 10-3, 1 × 10-2, 1.4 × 10-2, 5 × 10-2, and 0.1, respectively. Nucleosynthesis calculations are done using the NuGrid suite of codes, using a consistent nuclear reaction network between the models. Complete tables with yields and production factors are provided online at Zenodo:Yields (https://doi.org/10.5281/zenodo.8060323). We discuss the main properties of our yields in light of the present understanding of SN Ia nucleosynthesis, depending on different progenitor mass and composition. Finally, we compare our results with a number of relevant models from the literature

Type Ia Supernova Nucleosynthesis: Metallicity-Dependent Yields

Type Ia supernova explosions (SNIa) are fundamental sources of elements for the chemical evolution of galaxies. They efficiently produce intermediate-mass (with Z between 11 and 20) and iron group elements - for example, about 70% of the solar iron is expected to be made by SNIa. In this work, we calculate complete abundance yields for 39 models of SNIa explosions, based on three progenitors - a 1.4M deflagration detonation model, a 1.0 double detonation model and a 0.8 M double detonation model - and 13 metallicities, with 22Ne mass fractions of 0, 1x10-7, 1x10-6, 1x10-5, 1x10-4, 1x10-3, 2x10-3, 5x10-3, 1x10-2, 1.4x10-2, 5x10-2, and 0.1 respectively. Nucleosynthesis calculations are done using the NuGrid suite of codes, using a consistent nuclear reaction network between the models. Complete tables with yields and production factors are provided online at Zenodo: Yields. We discuss the main properties of our yields in the light of the present understanding of SNIa nucleosynthesis, depending on different progenitor mass and composition. Finally, we compare our results with a number of relevant models from the literature.Comment: 42 pages, 21 figures. Accepted for publication in ApJS 21-06-2

Catching Element Formation In The Act

Gamma-ray astronomy explores the most energetic photons in nature to address some of the most pressing puzzles in contemporary astrophysics. It encompasses a wide range of objects and phenomena: stars, supernovae, novae, neutron stars, stellar-mass black holes, nucleosynthesis, the interstellar medium, cosmic rays and relativistic-particle acceleration, and the evolution of galaxies. MeV gamma-rays provide a unique probe of nuclear processes in astronomy, directly measuring radioactive decay, nuclear de-excitation, and positron annihilation. The substantial information carried by gamma-ray photons allows us to see deeper into these objects, the bulk of the power is often emitted at gamma-ray energies, and radioactivity provides a natural physical clock that adds unique information. New science will be driven by time-domain population studies at gamma-ray energies. This science is enabled by next-generation gamma-ray instruments with one to two orders of magnitude better sensitivity, larger sky coverage, and faster cadence than all previous gamma-ray instruments. This transformative capability permits: (a) the accurate identification of the gamma-ray emitting objects and correlations with observations taken at other wavelengths and with other messengers; (b) construction of new gamma-ray maps of the Milky Way and other nearby galaxies where extended regions are distinguished from point sources; and (c) considerable serendipitous science of scarce events -- nearby neutron star mergers, for example. Advances in technology push the performance of new gamma-ray instruments to address a wide set of astrophysical questions.Comment: 14 pages including 3 figure

L1 Division and Differentiation Patterns Influence Shoot Apical Meristem Maintenance

Plant development requires regulation of both cell division and differentiation. The class 1 KNOTTED1-like homeobox (KNOX) genes such as knotted1 (kn1) in maize (Zea mays) and SHOOTMERISTEMLESS in Arabidopsis (Arabidopsis thaliana) play a role in maintaining shoot apical meristem indeterminacy, and their misexpression is sufficient to induce cell division and meristem formation. KNOX overexpression experiments have shown that these genes interact with the cytokinin, auxin, and gibberellin pathways. The L1 layer has been shown to be necessary for the maintenance of indeterminacy in the underlying meristem layers. This work explores the possibility that the L1 affects meristem function by disrupting hormone transport pathways. The semidominant Extra cell layers1 (Xcl1) mutation in maize leads to the production of multiple epidermal layers by overproduction of a normal gene product. Meristem size is reduced in mutant plants and more cells are incorporated into the incipient leaf primordium. Thus, Xcl1 may provide a link between L1 division patterns, hormonal pathways, and meristem maintenance. We used double mutants between Xcl1 and dominant KNOX mutants and showed that Xcl1 suppresses the Kn1 phenotype but has a synergistic interaction with gnarley1 and rough sheath1, possibly correlated with changes in gibberellin and auxin signaling. In addition, double mutants between Xcl1 and crinkly4 had defects in shoot meristem maintenance. Thus, proper L1 development is essential for meristem function, and XCL1 may act to coordinate hormonal effects with KNOX gene function at the shoot apex

An intracellular transcriptomic atlas of the giant coenocyte Caulerpa taxifolia.

Convergent morphologies have arisen in plants multiple times. In non-vascular and vascular land plants, convergent morphology in the form of roots, stems, and leaves arose. The morphology of some green algae includes an anchoring holdfast, stipe, and leaf-like fronds. Such morphology occurs in the absence of multicellularity in the siphonous algae, which are single cells. Morphogenesis is separate from cellular division in the land plants, which although are multicellular, have been argued to exhibit properties similar to single celled organisms. Within the single, macroscopic cell of a siphonous alga, how are transcripts partitioned, and what can this tell us about the development of similar convergent structures in land plants? Here, we present a de novo assembled, intracellular transcriptomic atlas for the giant coenocyte Caulerpa taxifolia. Transcripts show a global, basal-apical pattern of distribution from the holdfast to the frond apex in which transcript identities roughly follow the flow of genetic information in the cell, transcription-to-translation. The analysis of the intersection of transcriptomic atlases of a land plant and Caulerpa suggests the recurrent recruitment of transcript accumulation patterns to organs over large evolutionary distances. Our results not only provide an intracellular atlas of transcript localization, but also demonstrate the contribution of transcript partitioning to morphology, independent from multicellularity, in plants