scholarly journals The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

2019 ◽  
Author(s):  
Alexis R. Sullivan ◽  
Yrin Eldfjell ◽  
Bastian Schiffthaler ◽  
Nicolas Delhomme ◽  
Torben Asp ◽  
...  
Keyword(s):  
Norway Spruce ◽  
Vascular Plants ◽  
Recombination Rates ◽  
Mitochondrial Recombination ◽  
Highly Active ◽  
Mixed Support ◽  
Long Reads ◽  
Intramolecular Recombination ◽  
Key Aspects ◽  
Unusual Situation

AbstractPlant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pre-genome, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about a third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly-studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

scholarly journals The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

2019 ◽  
Vol 12 (1) ◽  
pp. 3586-3598 ◽  
Author(s):  
Alexis R Sullivan ◽  
Yrin Eldfjell ◽  
Bastian Schiffthaler ◽  
Nicolas Delhomme ◽  
Torben Asp ◽  
...  
Keyword(s):  
Norway Spruce ◽  
Vascular Plants ◽  
Recombination Rates ◽  
Mitochondrial Recombination ◽  
Highly Active ◽  
Mixed Support ◽  
Long Reads ◽  
Intramolecular Recombination ◽  
Key Aspects ◽  
Unusual Situation

Abstract Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

White Americans’ Opposition to Affirmative Action, Revisited: New Racism, Principled Objections, or Both?

2021 ◽  
pp. 232949652110246
Author(s):  
Matthew O. Hunt ◽  
Ryan A. Smith
Keyword(s):  
Affirmative Action ◽  
General Social Survey ◽  
First Century ◽  
White Americans ◽  
Short Article ◽  
Social Survey ◽  
Mixed Support ◽  
Primary Determinant ◽  
Preferential Hiring ◽  
Key Aspects

In this short article, we provide an update and extension of Thomas C. Wilson’s study, “Whites’ Opposition to Affirmative Action: Rejection of Group-based Preferences as well as Rejection of Blacks.” Wilson drew on data from the 1996 General Social Survey (GSS) to revisit a long-standing debate in the racial attitudes literature concerning whether anti-black prejudice (e.g., “new racism”) or ostensibly race-neutral opposition to group-based policies generally (i.e., “principled objections”) is the primary determinant of whites’ opposition to affirmative action in the form of “preferential hiring and promotion for blacks.” We analyze data from the 2000–2018 GSS to replicate and extend key aspects of Wilson’s work. As in the prior study, we find mixed support for the new racism and principled objections perspectives, providing an important update on white Americans’ beliefs about affirmative action for the twenty-first century.

scholarly journals A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera)

2019 ◽  
Author(s):  
Hanno Schmidt ◽  
Ann-Marie Waldvogel ◽  
Sören Lukas Hellmann ◽  
Barbara Feldmeyer ◽  
Thomas Hankeln ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Recombination Rate ◽  
Complete Mitochondrial Genome ◽  
Draft Genome ◽  
Chironomus Riparius ◽  
Recombination Rates ◽  
Biting Midge ◽  
Long Reads ◽  
Hybrid Genome ◽  
Genomic Studies

AbstractBackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.FindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.ConclusionsThe genome and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in detail. The estimated recombination rate will help evolutionary biologist gain a better understanding of commonalities and differences of genomic patterns in insects.

scholarly journals Vesicular storage, vesicle trafficking, and secretion of leptin and resistin: the similarities, differences, and interplays

2010 ◽  
Vol 206 (1) ◽  
pp. 27-36 ◽  
Author(s):  
Feng Ye ◽  
Aung Than ◽  
Yanying Zhao ◽  
Kian Hong Goh ◽  
Peng Chen
Keyword(s):  
Adipose Tissue ◽  
Protein Kinase ◽  
Vesicle Trafficking ◽  
Secretory Vesicles ◽  
Secretory Pathways ◽  
Endocrine Organ ◽  
Highly Active ◽  
Storage Vesicle ◽  
Key Aspects ◽  
Kinase A

Adipose tissue is a highly active endocrine organ secreting a variety of signaling molecules called adipokines. Leptin and resistin are two adipokines critically involved in metabolic homeostasis. Nevertheless, the secretory pathways of these adipokines and their interplays are poorly elucidated. In this work, we have comparatively studied several key aspects of leptin and resistin secretion from 3T3-L1 adipocytes. It was found that leptin and resistin molecules are compartmentalized into different secretory vesicles. The trafficking of leptin and resistin vesicles, and the secretion of leptin and resistin are oppositely regulated by insulin/glycolytic substrates and cAMP/protein kinase A. Interestingly, these two adipokines adversely influence each other on secretion and vesicle trafficking. Finally, we demonstrated that both leptin and resistin secretion are Ca2+ dependent.

scholarly journals Landscape-Scale Mixtures of Tree Species are More Effective than Stand-Scale Mixtures for Biodiversity of Vascular Plants, Bryophytes and Lichens

Forests ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 73 ◽  
Author(s):  
Steffi Heinrichs ◽  
Christian Ammer ◽  
Martina Mund ◽  
Steffen Boch ◽  
Sabine Budde ◽  
...  
Keyword(s):  
Norway Spruce ◽  
Scots Pine ◽  
Tree Species ◽  
Vascular Plants ◽  
European Beech ◽  
Landscape Scale ◽  
Gamma Diversity ◽  
Mixed Stands ◽  
Scale Mixtures ◽  
Species Mixtures

Tree species diversity can positively affect the multifunctionality of forests. This is why conifer monocultures of Scots pine and Norway spruce, widely promoted in Central Europe since the 18th and 19th century, are currently converted into mixed stands with naturally dominant European beech. Biodiversity is expected to benefit from these mixtures compared to pure conifer stands due to increased abiotic and biotic resource heterogeneity. Evidence for this assumption is, however, largely lacking. Here, we investigated the diversity of vascular plants, bryophytes and lichens at the plot (alpha diversity) and at the landscape (gamma diversity) level in pure and mixed stands of European beech and conifer species (Scots pine, Norway spruce, Douglas fir) in four regions in Germany. We aimed to identify compositions of pure and mixed stands in a hypothetical forest landscape that can optimize gamma diversity of vascular plants, bryophytes and lichens within regions. Results show that gamma diversity of the investigated groups is highest when a landscape comprises different pure stands rather than tree species mixtures at the stand scale. Species mainly associated with conifers rely on light regimes that are only provided in pure conifer forests, whereas mixtures of beech and conifers are more similar to beech stands. Combining pure beech and pure conifer stands at the landscape scale can increase landscape level biodiversity and conserve species assemblages of both stand types, while landscapes solely composed of stand scale tree species mixtures could lead to a biodiversity reduction of a combination of investigated groups of 7 up to 20%.

scholarly journals Binary recombinase systems for high-resolution conditional mutagenesis

2014 ◽  
Vol 42 (6) ◽  
pp. 3894-3907 ◽  
Author(s):  
Mario Hermann ◽  
Patrick Stillhard ◽  
Hendrik Wildner ◽  
Davide Seruggia ◽  
Viktor Kapp ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Cell Lineage ◽  
Cell Types ◽  
Cre Recombinase ◽  
Lineage Tracing ◽  
Recombination Rates ◽  
Highly Active ◽  
Conditional Mutagenesis ◽  
Trans Splicing ◽  
Optimal Efficiency

Abstract Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.

scholarly journals A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera)

2020 ◽  
Vol 10 (4) ◽  
pp. 1151-1157 ◽  
Author(s):  
Hanno Schmidt ◽  
Sören Lukas Hellmann ◽  
Ann-Marie Waldvogel ◽  
Barbara Feldmeyer ◽  
Thomas Hankeln ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Recombination Rate ◽  
Complete Mitochondrial Genome ◽  
Draft Genome ◽  
Chironomus Riparius ◽  
Recombination Rates ◽  
Biting Midge ◽  
Long Reads ◽  
Hybrid Genome ◽  
Genomic Studies

Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombination rates at all. The genome assembly and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in particular. The estimated recombination rate will help evolutionary biologists gaining a better understanding of commonalities and differences of genomic patterns in insects.

scholarly journals Palladium-Catalyzed Nondirected Late-Stage C-H Deuteration of Arenes

2021 ◽  
Author(s):  
Mirxan Farizyan ◽  
Arup Mondal ◽  
Sourjya Mal ◽  
Fritz Deufel ◽  
Manuel van Gemmeren
Keyword(s):  
Late Stage ◽  
Functional Group ◽  
Bidentate Ligands ◽  
Isotopic Labelling ◽  
Deuterium Incorporation ◽  
Highly Active ◽  
Palladium Catalyzed ◽  
Development Processes ◽  
Key Aspects ◽  
Sulfonamide Group

We describe a palladium catalyzed non-directed late-stage deuteration of arenes. Key aspects include the use of D2O as a convenient and easily available deuterium source and the discovery of highly active N,N-bidentate ligands containing an N-acyl sulfonamide group. The reported protocol enables high degrees of deuterium incorporation via a reversible C-H activation step and features an extraordinary functional group tolerance, allowing for the deuteration of complex substrates. This is exemplified by the late-stage isotopic labelling of various pharmaceutically relevant motifs and related scaffolds. We expect that this method, amongst other applications, will prove useful as a tool in drug development processes and for mechanistic studies.

scholarly journals Arabidopsis high temperature stress research

2018 ◽  
Vol 87 (3) ◽  
Author(s):  
Alicja Dolzblasz ◽  
Sylwia Dołzbłasz
Keyword(s):  
Stem Cells ◽  
Arabidopsis Thaliana ◽  
Vascular Plants ◽  
Apical Meristem ◽  
Heat Waves ◽  
Short Review ◽  
High Temperature Stress ◽  
Molecular Response ◽  
Key Aspects ◽  
The Impact

The rise in global temperature and increasingly frequent heat waves may severely disturb plant growth and productivity. Throughout the life cycle of vascular plants, which may last even thousands of years, various aboveground structures are constructed due to the activity of the shoot apical meristem (SAM). A pool of dividing, undifferentiated stem cells is maintained within a SAM, which facilitates self-perpetuation of the meristem and provides cells for growth and organogenesis. Unsurprisingly, there has been a growing interest to study the impact of increased temperatures on the development and molecular response of the model plant <em>Arabidopsis thaliana</em>. Unfortunately, the experimental setups are highly variable and key aspects of plant development are regularly neglected. Thus, in this short review, we highlight the experimental variables and address SAM maintenance in the context of elevated temperature research.

A Scanning Electron Microscopic Study of Pro-Vascular Cellular Morphology in Chaetophora Incressata

1985 ◽  
Vol 43 ◽  
pp. 638-639
Author(s):  
A. E. Hotchkiss ◽  
A. T. Hotchkiss ◽  
R. P. Apkarian
Keyword(s):  
Green Algae ◽  
Vascular Plants ◽  
Vascular System ◽  
Higher Plants ◽  
Wall Structure ◽  
Electron Microscopic ◽  
Physiological Processes ◽  
Scanning Electron Microscopic Study ◽  
Scanning Electron Microscopic ◽  
Scanning Electron

Multicellular green algae may be an ancestral form of the vascular plants. These algae exhibit cell wall structure, chlorophyll pigmentation, and physiological processes similar to those of higher plants. The presence of a vascular system which provides water, minerals, and nutrients to remote tissues in higher plants was believed unnecessary for the algae. Among the green algae, the Chaetophorales are complex highly branched forms that might require some means of nutrient transport. The Chaetophorales do possess apical meristematic groups of cells that have growth orientations suggestive of stem and root positions. Branches of Chaetophora incressata were examined by the scanning electron microscope (SEM) for ultrastructural evidence of pro-vascular transport.

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