An auxin-mediated ultradian rhythm promotes root regeneration in Arabidopsis

Abstract Ultradian rhythms have been proved to be critical for diverse biological processes. However, comprehensive understanding of the short-period rhythms remains limited. Here, we discover that leaf excision triggers a gene expression rhythm with ~ 3-h periodicity, named as the excision ultradian rhythm (UR), which is regulated by the plant hormone auxin. Transcriptome analysis found more than 4,000 excision UR genes which are diverse in terms of biological function. Promoter–luciferase analyses showed that the spatiotemporal patterns of the excision UR were positively associated with de novo root regeneration (DNRR), a post-embryonic developmental process. Genetic studies showed that EXCISION ULTRADIAN RHYTHM 1 (EUR1), which encodes ENHANCER OF ABSCISIC ACID CO-RECEPTOR1 (EAR1), an abscisic acid signaling regulator, was required to generate the excision ultradian rhythm and promote root regeneration. Moreover, the ear1 mutant exhibited the absence of auxin-induced excision UR generation and partial failure to rescue DNRR. These results demonstrate that leaf excision activates EAR1-mediated excision UR and reprograms the expression of a large set of genes involved in DNRR.

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Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Forests ◽

10.3390/f12020222 ◽

2021 ◽

Vol 12 (2) ◽

pp. 222

Author(s):

Bartosz Ulaszewski ◽

Joanna Meger ◽

Jaroslaw Burczyk

Keyword(s):

Population Genomics ◽

De Novo ◽

Genetic Studies ◽

Genomic Libraries ◽

Reduced Representation ◽

Large Numbers ◽

Broadleaved Tree Species ◽

Fagus Sylvatica L ◽

Reference Genomes ◽

Future Population

Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

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Hormone Orchestrates a Hierarchical Transcriptional Cascade That Regulates Al-Induced De Novo Root Regeneration in Tea Nodal Cutting

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.1c01100 ◽

2021 ◽

Author(s):

Long Cheng ◽

Huan Liu ◽

Jing Zhao ◽

Yuan Dong ◽

Qingshan Xu ◽

...

Keyword(s):

De Novo ◽

Root Regeneration ◽

Nodal Cutting

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Taube nuss is a novel gene essential for the survival of pluripotent cells of early mouse embryos

Development ◽

10.1242/dev.127.24.5449 ◽

2000 ◽

Vol 127 (24) ◽

pp. 5449-5461 ◽

Cited By ~ 1

Author(s):

A.K. Voss ◽

T. Thomas ◽

P. Petrou ◽

K. Anastassiadis ◽

H. Scholer ◽

...

Keyword(s):

Cell Population ◽

Developmental Process ◽

Inner Cell Mass ◽

Chromatin Condensation ◽

Cell Mass ◽

Adult Brain ◽

Stem Cell Population ◽

Novel Gene ◽

Stage Of Development ◽

Short Period

The cells of the inner cell mass constitute the pluripotent cell population of the early embryo. They have the potential to form all of the tissues of the embryo proper and some extra-embryonic tissues. They can be considered a transient stem cell population for the whole of the embryo, and stem cells maintaining the same capacity can be isolated from these cells. We have isolated, characterised and mutated a novel gene, taube nuss (Tbn), that is essential for the survival of this important cell population. The taube nuss protein sequence (TBN) was highly conserved between human, mouse, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana, particularly in a domain that is not present in any published proteins, showing that TBN is the founding member of a completely new class of proteins with an important function in development. The Tbn gene was expressed ubiquitously as early as E2. 5 and throughout embryonic development. It was also expressed in adult brain with slightly higher levels in the hippocampus. The Tbn mutant embryos developed normally to the blastocyst stage and contained inner cell masses. They hatched from the zonae pellucidae, implanted and induced decidual reactions, but failed to develop beyond E4.0. At this time the trophoblast cells were viable, but inner cell masses were not detectable. At E3.75, massive TUNEL-positive DNA degradation and chromatin condensation were visible within the inner cell masses, whereas the cell membranes where intact. Caspase 3 was expressed in these cells. In vitro, the inner cell mass of mutant embryos failed to proliferate and died after a short period in culture. These results indicate that the novel protein, taube nuss, is necessary for the survival of the inner cell mass cells and that inner cell mass cells died of apoptosis in the absence of the taube nuss protein. As cell pruning by apoptosis is a recognised developmental process at this stage of development, the taube nuss protein may be one of the factors regulating the extent of programmed cell death at this time point.

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Antithrombotic strategy in patients with atrial fibrillation and acute coronary syndrome

European Heart Journal ◽

10.1093/eurheartj/ehab724.1485 ◽

2021 ◽

Vol 42 (Supplement_1) ◽

Author(s):

I Almeida ◽

H Santos ◽

M Santos ◽

H Miranda ◽

J Chin ◽

...

Keyword(s):

Atrial Fibrillation ◽

Vitamin K ◽

Antithrombotic Therapy ◽

De Novo ◽

Vitamin K Antagonists ◽

Antiplatelet Agent ◽

P2y12 Inhibitors ◽

Coronary Syndrome ◽

Short Period ◽

St Elevation

Abstract Background Atrial fibrillation (AF) is frequent in patients admitted with acute coronary syndromes (ACS). The development of this arrhythmia occurs in 2–21% of patients with non ST-elevation ACS and 21% of ST-elevation ACS. According with the most recent European guidelines, a short period up to 1 week of triple antithrombotic therapy (TAT) is recommended, followed by dual antithrombotic therapy (DAT) using a NOAC and a single antiplatelet agent, preferably clopidogrel. Objective To compare the antithrombotic strategy (DAT vs TAT) used and its prognostic value in patients with AF and ACS. Methods Retrospective analysis of patients' data admitted with ACS in a multicentric registry between 10/2010–09/2019. TAT was defined as the prescription of dual antiplatelet therapy and one anticoagulant and DAT as one antiplatelet and one anticoagulant. Survival and rehospitalization were evaluated through Kaplan-Meier curve. Results 1067 patients were included, mean age 67±14 years, 72.3% male. Patients who developed de novo AF during hospitalization due to ACS were older (75±12 vs 66±14 years, p<0.001) and with higher prevalence of cardiovascular risk factors and cardiovascular disease. AF was more often in patients with ST elevation ACS (53.4%). During hospitalization, AF patients were more often medicated with aspirin, glycoprotein inhibitor, heparin, fondaparinux and vitamin K antagonists. No difference was found regarding P2Y12 inhibitors. AF patients presented more often obstructive coronary disease (normal coronaries 5.4 vs 8.5%, p<0.001) so they were more often submitted to PCI (79.5 vs 70.9%, p<0.001). AF patients presented with higher rates of adverse in-hospital events as re-infarction, heart failure, shock, ventricular arrhythmias, cardiac arrest, stroke, major bleeding and death (p<0.001). At discharge, AF patients were less prescribed with aspirin or ticagrelor, but the rate of clopidogrel prescription was higher, such as vitamin K antagonists or any of the new anticoagulants. In the AF group, 21.5% patients were discharged with TAT and 30.3% with DAT. Concerning patients discharged with TAT, 1-year follow-up revealed no significant differences in mortality (p=0.578), re-admission for cardiovascular causes (p=0.301) and total re-admission rates (p=0.291). Patients discharged with DAT had similar mortality (p=0.623) and re-admission for cardiovascular causes rates (p=0.138), but significant differences were identified regarding total re-admissions (p=0.024). Conclusions In patients with ACS and de novo AF, a low percentage of patients was discharged with oral anticoagulation (51.8%). In those whose anticoagulation was initiated, DAT was the preferred strategy. 1-year outcomes were not different between the antithrombotic strategy, except for all cause re-admission. FUNDunding Acknowledgement Type of funding sources: None.

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A Systematic Review on Extreme Phenotype Strategies to Search for Rare Variants in Genetic Studies of Complex Disorders

10.20944/preprints202007.0583.v1 ◽

2020 ◽

Author(s):

Sana Amanat ◽

Teresa Requena ◽

Jose Antonio Lopez-Escamez

Keyword(s):

Systematic Review ◽

Candidate Genes ◽

Rare Variants ◽

De Novo ◽

Complex Diseases ◽

De Novo Mutations ◽

Genetic Studies ◽

Complex Disorders ◽

Extreme Phenotype ◽

Age Related

Exome sequencing has been commonly used in rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) to search for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to heritability in complex clinical traits. We have conducted a systematic review to find evidence supporting the use of EP strategies to search for rare variants in genetic studies of complex diseases, to highlight the contribution of rare variation to the genetic structure of multiallelic conditions. After performing the quality assessment of the retrieved records, we selected 19 genetic studies considering EP to demonstrate genetic association. All the studies successfully identified several rare variants, de novo mutations and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach in patients with an early onset of the disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.

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Decomposition of food waste using bulking agent and bio-drying technology

E3S Web of Conferences ◽

10.1051/e3sconf/20187305013 ◽

2018 ◽

Vol 73 ◽

pp. 05013

Author(s):

Oktiawan Wiharyanto ◽

Hadiwidodo Mochtar ◽

Bagus Priyambada Ika ◽

Purwono Purwono

Keyword(s):

Food Waste ◽

Bulking Agent ◽

Biological Processes ◽

Compost Maturity ◽

Short Period ◽

Long Time ◽

Mature Compost ◽

Biological Decomposition ◽

Drying Technology ◽

Maturity Parameters

Technology to process food waste should be easy maintenance, fast, economical, affordable, environmentally friendly, and socially acceptable. Processing food waste according to the principle is biological decomposition. Biological processes usually take quite a long time (30 days). This study aims to accelerate the process of decomposition of food waste and produce a quality fertilizer products. Bulking agent (biofilm), bio activator (microorganism from cassava), and bio-drying technology are used to accelerate the decomposition process. The ratio of food waste and bulking agent is 7:3 (v/v). Mature product serves as a bulking agent and additive microorganisms. Additive microorganisms are also done by adding microorganism derived from cassava with a ratio of 10ml/500 g (Ml); 20 ml/500 g (M2); and 10ml/500 g of food waste (M3). The results showed the temperature of the food waste reached 50 ? at first. The addition of bulking agent and Additive microorganisms causes the thermophilic phase to occur early. This shows the thermophilic phase being achieved in a short period. Based on testing of compost maturity parameters, food waste has matured within 3 days. The C-Organic Concentration was 27.57%, N-total 1.98%, C/N ratio of 13.92, P-Total 0.23% and K-total 0.83%. In conclusion of this study, mature compost can be used as bulking agent with mature compost ratio and 7: 3 (v/v) bulking agent. Processing food waste is quite effective using a combination of bulking agent (mature compost), additive microorganisms and bio-drying technology.

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Potato cold hardiness development and abscisic acid. II. De novo synthesis of proteins is required for the increase in free abscisic acid during potato (Solanum commersonii) cold acclimation

Physiologia Plantarum ◽

10.1034/j.1399-3054.1994.900104.x ◽

1994 ◽

Vol 90 (1) ◽

pp. 21-26 ◽

Cited By ~ 1

Author(s):

Stephen B. Ryu ◽

Paul H. Li

Keyword(s):

Abscisic Acid ◽

Cold Acclimation ◽

Cold Hardiness ◽

De Novo ◽

De Novo Synthesis ◽

Solanum Commersonii

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Potato cold hardiness development and abscisic acid. II. De novo synthesis of proteins is required for the increase in free abscisic acid during potato (Solanum commersonii) cold acclimation

Physiologia Plantarum ◽

10.1111/j.1399-3054.1994.tb02187.x ◽

1994 ◽

Vol 90 (1) ◽

pp. 21-26 ◽

Cited By ~ 7

Author(s):

Stephen B. Ryu ◽

Paul H. Li

Keyword(s):

Abscisic Acid ◽

Cold Acclimation ◽

Cold Hardiness ◽

De Novo ◽

De Novo Synthesis ◽

Solanum Commersonii

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Mining, characterization and application of transcriptome-based SSR markers in Chinese jiaotou

Plant Genetic Resources ◽

10.1017/s1479262117000338 ◽

2018 ◽

Vol 16 (4) ◽

pp. 306-314

Author(s):

Chan Liu ◽

Qing Tang ◽

Chaohua Cheng ◽

Ying Xu ◽

Zemao Yang ◽

...

Keyword(s):

Ssr Markers ◽

Large Scale ◽

Trinucleotide Repeat ◽

De Novo ◽

Local Varieties ◽

Genetic Studies ◽

Oxidation Reduction ◽

Ssr Loci ◽

Wild Accessions ◽

Expressed Sequence

AbstractChinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembledde novoby a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

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