scholarly journals An Improved Assembly Strategy Helps Parsing the Cryptic Mitochondrial Genome Evolution in Plants

2021 ◽  
Author(s):  
Yanlei Feng ◽  
Xiaoguo Xiang ◽  
Delara Akhter ◽  
Zhixi Fu ◽  
Ronghui Pan ◽  
...  
Keyword(s):  
Intermediate Stage ◽  
Third Party ◽  
Mitochondrial Genomes ◽  
Seed Plant ◽  
High Quality ◽  
Mitochondrial Plasmid ◽  
Assembly Strategy ◽  
Mitochondrial Genome Evolution ◽  
Almost All ◽  
Considerable Complexity

Abstract Although plant mitochondrial genomes (mitogenomes) are small, they exhibit considerable complexity not seen in other eukaryotic mitogenomes. Assembly and analysis of plant mitogenomes is hampered by their large variations in structure and size, and the mitogenome remains the last genome to be deciphered in many plant species. As a result, very few plant mitogenomes have been assembled and little is known regarding their evolution. In this study, a strategy was devised for assembly of mitogenomes from existing short reads from whole-genome sequencing projects. The strategy combined current tools and manual steps to resolve the two main challenges to mitogenome assembly: repeat and plastid insertion sequences. High-quality complete mitogenomes were assembled for 23 species from five families of the Fagales. Mitogenomes varied 2.4 times in size. The largest, Carpinus cordata, did not contain large amounts of unique sequences, but instead contained a high proportion of sequences homologous to other Fagales. Further analysis of the Fagales mitogenomes revealed highly mosaic characteristics, with horizonal transfer (HGT)-like sequences identified from almost all seed plant taxa. Independent and unequal transfers of third-party DNA may partially account for the HGT-like fragments and unbalanced size expansions observed in Fagales mitogenomes. Supporting this, a mitochondrial plasmid of nuclear origin was found in Carpinus, and this may represent an intermediate stage prior to incorporation into the mitogenome. The approaches used in this study are widely applicable and provide new insights into the mechanisms of mitogenome evolution in plants.

scholarly journals 344 The Ag Guide serves as a primary standard for animal scientists and AAALAC accreditation of Ag research programs

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 71-72
Author(s):  
Janeen Salak-Johnson
Keyword(s):  
Animal Welfare ◽  
Primary Standard ◽  
Animal Research ◽  
Third Party ◽  
Best Interests ◽  
Professional Judgment ◽  
High Quality ◽  
Accreditation Program ◽  
Agricultural Animal ◽  
Animal Care

Abstract Institutions that engage in animal research and production must ensure that high standards of animal care and use meet expectations of society while being ethical stewards of the animals they use in research. In order to achieve engagement in best practices, the Ag Guide is the most appropriate standard for assessing agricultural animals used in research and teaching. The Ag Guide minimizes the potential to overuse performance standards while enhancing the ability to appropriately address specific performance-derived exceptions to situations for which they have been validated. The primary objectives of the standards established in the Ag Guide are well-aligned with the goals of the AAALAC International accreditation program. The Ag Guide provides scientifically-sound, performance-based approaches to animal care and housing, which meet the expectations of AAALAC’s accreditation program. AAALAC provides a third-party peer review of all facets of the animal care and use program that serves as an effective mechanism to ensure institutions meet the standards of the Ag Guide. The process is designed to help identify the strengths and weaknesses of the program to ensure high-quality scientific outcomes and a high level of animal welfare. AAALAC accreditation program for agricultural animal research program is built on the cornerstone of the Ag Guide standards and connects science and responsible animal care. AAALAC accreditation promotes a comprehensive, institutionally supported program with a commitment to continuous improvement, humane and ethical animal care resulting in high-quality animal welfare, and scientific validity. AAALAC takes the position that, in accredited programs, the housing and care for agricultural animals should meet the standards that prevail on a high-quality, well-managed farm and the Ag Guide serves as this foundation. Therefore, the use of the Ag Guide for agricultural animal programs ensures a review that is based on science, professional judgment, and the best interests of the animal.

scholarly journals Mineral Element Deposition and Gene Expression across Different Tissues of Cherry Valley Ducks

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 238
Author(s):  
Qianqian Song ◽  
Yi Zhang ◽  
Hao Bai ◽  
Li Zhong ◽  
Xiaofan Li ◽  
...  
Keyword(s):  
Significant Negative Correlation ◽  
Mineral Elements ◽  
Breast Muscle ◽  
Thigh Muscle ◽  
Mrna Levels ◽  
High Quality ◽  
Atomic Fluorescence ◽  
Breeding Efficiency ◽  
Almost All ◽  
Different Tissues

This study was conducted to investigate the deposition of several mineral elements and the mRNA levels of mineral-related genes across different tissues of cherry valley ducks. The contents of magnesium (Mg), potassium (K), zinc (Zn), and selenium (Se) in ducks’ breast muscle, thigh muscle, liver, skin, and tibia at the age of 0, 21, 35, 49, and 63 days, respectively, were measured using an atomic fluorescence spectrophotometer, while the mRNA levels of mineral-related genes were detected by qRT-PCR. The results revealed that the dynamics of Mg and K were generally similar in each tissue, with a significant positive correlation (p < 0.05). In the breast muscle, thigh muscle, and liver, the contents of almost all mineral elements reached their peak values (p < 0.05) at the age of 49 to 63 days. Interestingly, the expression of most mineral-related genes was the highest at birth (p < 0.05). In addition, there was a significant negative correlation between the expression of ATP1A1 and the deposition of K (r = −0.957, p < 0.05), and a similar result was found for the expression of ATP8 and the deposition of Zn (r = −0.905, p < 0.05). Taken together, Mg and K could be used as joint indicators for the precise breeding of the high-quality strain of cherry valley ducks, while the age of 49 to 63 days could be used as the reference for the best marketing age. In addition, ATP1A1 and ATP8 could be used as the key genes to detect K and Zn, respectively. Hence, the findings of this study can be used to improve the production and breeding efficiency of high-quality meat ducks.

Enkev Beheer BV (of the Netherlands) v. Republic of Poland

ICSID Reports ◽  
2021 ◽  
Vol 19 ◽  
pp. 630-648
Keyword(s):  
Due Process ◽  
The State ◽  
Third Party ◽  
Waiting Period ◽  
Content Type ◽  
Fair And Equitable Treatment ◽  
Just Compensation ◽  
Default Rules ◽  
Equitable Treatment ◽  
Almost All

630Procedure — Addition of a party — Conditional application — UNCITRAL Rules, Article 22 — UNCITRAL Rules, Article 17 — Whether the UNCITRAL Rules or lex loci arbitri allowed for applications to be made conditional on a tribunal’s future decision — Whether the application was consistent with the State’s procedural rights — Whether the amendment to a claim under Article 22 of the UNCITRAL Rules allowed for the addition of a third party as claimantJurisdiction — Investment — Shares — Whether an investor’s shares and rights derived from those shares were protected investments under the BITJurisdiction — Investment — Assets of subsidiary — Whether profits, goodwill or know-how of a local subsidiary constituted investments of the investor protected by the BITJurisdiction — Consent — Cooling-off period — Premature claims — Whether the investor had communicated its own claims rather than those of its local subsidiary — Whether the investor’s failure to comply with a waiting period of six months under the BIT required a tribunal to deny jurisdiction or admissibility — Whether the negotiation of a local subsidiary’s dispute in good faith was relevant to jurisdiction over a foreign investor’s claimsInterpretation — Cooling-off period — VCLT, Article 31 — Object and purpose — Whether the object and purpose of the BIT required a tribunal not to adopt a strict or formalistic interpretation of the waiting period of six monthsRemedies — Declaratory award — Interpretation — Just compensation — Whether the tribunal had jurisdiction under the BIT to make a declaratory award on the interpretation and application of the term “just compensation”Jurisdiction — Dispute — Whether the tribunal had jurisdiction under the BIT to advise the parties of an imminent disputeExpropriation — Direct deprivation — Shares — Rights derived from shares — Whether the State directly deprived the investor of its rights as a shareholder in its local subsidiaryExpropriation — Indirect deprivation — Shares — Rights derived from shares — Whether the shares had lost all or almost all significant commercial value — Whether the measures were adopted in the public interest — Whether due process had been followed — Whether there were any undertakings by the StateExpropriation — Interpretation — “Just compensation” — Whether there was any difference between the terms of the BIT and general international law — Whether the meaning of just compensation could be determined in the abstract631Fair and equitable treatment — Whether the impending expropriation constituted a breach of the standard of fair and equitable treatment — Whether the claim concerned the investor’s rights derived from sharesFull protection and security — Whether the State failed to protect an investment from expropriation by local authorities — Whether the claim concerned the investor’s rights derived from sharesUmbrella clause — Whether there was any assurance directed at the investor that created any legal obligations — Whether the claim concerned the investor’s rights derived from sharesCosts — Arbitration costs — Variation by agreement — UNCITRAL Rules — Whether the terms of the BIT varied the default rules for the allocation of arbitration costs

scholarly journals Modelling Perceived Risks Associated to the Entry of Complementors’ in Platform Enterprises: A Case Study

2018 ◽  
Vol 10 (9) ◽  
pp. 3272 ◽  
Author(s):  
Elena-Teodora Miron ◽  
Anca Purcarea ◽  
Olivia Negoita
Keyword(s):  
Literature Review ◽  
Perceived Risk ◽  
Asset Specificity ◽  
Third Party ◽  
High Quality ◽  
Perceived Risks ◽  
Proposed Model ◽  
Perceived Environmental Uncertainty ◽  
Main Attraction

Third-party innovators, i.e., complementors, in platform enterprises develop and commercialize add-on products which are one of the main attraction points for customers. To ensure a sustainable evolution of the enterprise, the platform owner needs to attract and retain high-quality third-party innovators. We posit that the transaction costs incurred upon joining the enterprise as well as the controls imposed by the platform owner throughout the development and commercialization process shape the innovator’s perceived risk and influence his decision on whether to join or not. Based on a literature review, the paper at hand proposes a conceptual model for complementors to assess their perceived risk and subsequently evaluates the model in a case study of a platform enterprise for IT-based modelling tools. While some of the propositions are validated, i.e., that informational controls decrease the perceived environmental uncertainty and implicitly the perceived risks, other propositions, such as the fact that asset specificity is a deterrent to entering the platform enterprise could not be validated. Further case studies are necessary to provide a conclusive proof of the proposed model.

scholarly journals Semi-Supervised Multi-View Clustering with Weighted Anchor Graph Embedding

2021 ◽  
Vol 2021 ◽  
pp. 1-22
Author(s):  
Senhong Wang ◽  
Jiangzhong Cao ◽  
Fangyuan Lei ◽  
Qingyun Dai ◽  
Shangsong Liang ◽  
...  
Keyword(s):  
State Of The Art ◽  
Graph Embedding ◽  
Multiple Views ◽  
Time Cost ◽  
Practical Application ◽  
Real World Data ◽  
High Quality ◽  
Free Graph ◽  
Anchor Points ◽  
Almost All

A number of literature reports have shown that multi-view clustering can acquire a better performance on complete multi-view data. However, real-world data usually suffers from missing some samples in each view and has a small number of labeled samples. Additionally, almost all existing multi-view clustering models do not execute incomplete multi-view data well and fail to fully utilize the labeled samples to reduce computational complexity, which precludes them from practical application. In view of these problems, this paper proposes a novel framework called Semi-supervised Multi-View Clustering with Weighted Anchor Graph Embedding (SMVC_WAGE), which is conceptually simple and efficiently generates high-quality clustering results in practice. Specifically, we introduce a simple and effective anchor strategy. Based on selected anchor points, we can exploit the intrinsic and extrinsic view information to bridge all samples and capture more reliable nonlinear relations, which greatly enhances efficiency and improves stableness. Meanwhile, we construct the global fused graph compatibly across multiple views via a parameter-free graph fusion mechanism which directly coalesces the view-wise graphs. To this end, the proposed method can not only deal with complete multi-view clustering well but also be easily extended to incomplete multi-view cases. Experimental results clearly show that our algorithm surpasses some state-of-the-art competitors in clustering ability and time cost.

scholarly journals Bathymetric surveys of Shpilje reservoir

2018 ◽  
Vol 16 (1) ◽  
pp. 149-157
Author(s):  
Dragan Ivanoski ◽  
Slavisa Trajkovic ◽  
Milan Gocic
Keyword(s):  
High Quality ◽  
Field Surveys ◽  
Republic Of Macedonia ◽  
Artificial Lakes ◽  
The Republic ◽  
Almost All ◽  
Basin Area ◽  
Regular Practice

Periodic bathymetric surveys are carried out to define quantity of sedimented material in reservoirs, as well as to determine the areas most endangered by the silting process. Such surveys in the Republic of Macedonia were started as an obligatory and regular practice in the seventies of the last century, immediately after the formation of the larger artificial lakes. These were carried out for almost all reservoirs in the country and it can be said that there is already a sufficient amount of data on some of them that can serve as a basis for high quality analyses of the silting trend of the reservoirs and of the extent to which erosion is affecting the basin area. This paper provides a review of the results from the latest field surveys and analyses of changes in the configuration of the Shpilje reservoir bottom, carried out in the period 2014 to 2016.

scholarly journals Multielement analysis of plant extracts with potential use in the treatment of peptic ulcers by synchrotron radiation total reflection X-ray fluorescence

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5375
Author(s):  
Leticia Diniz Vieira ◽  
Káthia Takeda da Silva ◽  
Rodrigo Sanchez Giarola ◽  
Guilherme Franco Inocente ◽  
Hélio Kushima ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Intermediate Stage ◽  
Total Reflection ◽  
New Drugs ◽  
Peptic Ulcers ◽  
X Ray ◽  
Analytical Technique ◽  
Methanolic Extracts ◽  
Synchrotron Light ◽  
Almost All

Some plants popularly employed for the treatment of peptic ulcers have proved to be attractive sources of new drugs. Despite extensive research, the pharmacological and toxicological potentials of these plants are not fully understood. In this context, the aim of this work was to analyze the multielemental composition of the methanolic extracts of three of those plants, Alchornea glandulosa (AG), Davilla elliptica (DE) and Davilla nitida (DN), with the intention of contributing to the understanding of the mechanisms of action of these extracts. For this purpose, we used the analytical technique of total reflection X-ray fluorescence (TXRF) by synchrotron radiation at the Brazilian Synchrotron Light Source (LNLS/CNPEM). It was possible to determine the concentrations of the elements: P, S, Cl, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Rb and Br in all of the samples. Selenium (Se) was detected only in the DN extract. An inverse relationship between the concentrations of elements with proven effectiveness and the gastroprotective activity of extracts considering induction protocols with ethanol and non-steroidal anti-inflammatory drugs (NSAIDs) was obtained. This data suggests that the function of the extract is not only associated with providing the elements for restoring the gastric mucosa but that it also promotes the displacement of these elements from other parts of the mucosa to the damaged area. Correlations between the concentrations of the elements were also obtained. In the DE extract, which is the most effective extract for both induction protocols, the obtained correlations were above 70% among almost all of the elements, and no anticorrelations were found. For the other two extracts, in the less effective extract (AG) anticorrelations above 70% were predominantly found. Meanwhile, in the DN extract, a few high anticorrelations were found, which may explain its intermediate stage of effectiveness.

Production of and Supply of the Army with Small Arms on the Eve of the Russo-Turkish War (1877–1878). A Brief Overview of the Russian Military Industry

Epohi ◽  
2021 ◽  
Vol 29 (2) ◽  
Author(s):  
Simeon Tsvetkov ◽  
Keyword(s):  
Crimean War ◽  
High Quality ◽  
Military Industry ◽  
Small Arms ◽  
Russian Army ◽  
Main System ◽  
Short Period ◽  
Russian Military ◽  
Almost All

In the wake of the Crimean War, the upper military circles in Russia changed their thinking with regard to firearms. General Milyutin became Minister of War. It was the time when Alexander II reigned over Russia. In 1856, the calibre of Russian firearms was reduced to 6 inches, or 15.24 mm. The process of re-equipping the Russian army with M1856 rifles using expanding Minié bullets was launched. These rifles demonstrated that the percussion systems had reached the limit of their capacity for improvement. Nothing else could be improved in terms of their firing speed. Despite the resistance of the conservative military circles, Milyutin encouraged new inventions, and the 1860s became a period of experimentation with firearms. Some new cartridge systems were introduced. The high-quality M1856 percussion rifle was not destined to take part in war times, but the Russian army had been fully equipped with it for a short period of time. Almost all systems of the 1860s were based on this rifle. Over 10 systems of firearms with an internal needle fuse were proposed to the weapons commission. In 1866, the Englishman Karle proposed his own system with an internal needle fuse. Krnka, Berdan I, and Berdan II came next. After 1866, the Terry-Norman, Karle, and Krnka rifles entered the Russian army. These systems were developed on the basis of the 6-line M1856/58 rifle. The latter was converted into a rear-loading rifle. In 1869, the Krnka rifle was chosen as the main system, which became the main weapon of the Russian army in the following years. At the beginning of 1877, there were 613,297 Krnka rifles, 150,868 Karle rifles, 17,810 Berdan I and 325,254 Berdan II rifles in the Russian army.

scholarly journals Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

2019 ◽  
Vol 11 (7) ◽  
pp. 1797-1812 ◽  
Author(s):  
Dong Zhang ◽  
Hong Zou ◽  
Cong-Jie Hua ◽  
Wen-Xiang Li ◽  
Shahid Mahboob ◽  
...  
Keyword(s):  
Life Histories ◽  
Phylogenetic Reconstruction ◽  
Mitochondrial Genomes ◽  
Data Sets ◽  
Long Branch Attraction ◽  
Mitochondrial Data ◽  
Gc Skew ◽  
Limited Applicability ◽  
Phylogenetic Hypotheses ◽  
Almost All

Abstract The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

Sign in / Sign up

Export Citation Format

Share Document