Discovering Models for State-based Processes

M.L. van Eck,N. Sidorova,W.M.P. van der Aalst 대한산업공학회 2016 대한산업공학회 춘계학술대회논문집 Vol.2016 No.4

Discovering Models for State-based Processes

M.L. van Eck,N. Sidorova,W.M.P. van der Aalst 한국경영과학회 2016 한국경영과학회 학술대회논문집 Vol.2016 No.4

Risk Factors for Failure of Nonoperative Treatment for Unilateral Cervical Facet Fractures

Carola Francisca van Eck,Mitchell Stephen Fourman,Amir Mohamad Abtahi,Louis Alarcon,William Fielding Donaldson,Joon Yung Lee 대한척추외과학회 2017 Asian Spine Journal Vol.11 No.3

Study Design: Retrospective clinical study. Purpose: The purpose of this study was to determine what percentage of patients who underwent nonoperative management of unilateral non-displaced or minimally displaced facet fractures progressed radiographically and to determine what percentage of patients required surgical intervention and to identify risk factors for failure of conservative management. Overview of Literature: According to most commonly used classification systems, unilateral, non-and minimally displaced facet fractures are be amendable to nonoperative management. Methods: A retrospective review of the Trauma Registry of a Level I trauma center was performed to identify all patients diagnosed with a non- or minimally displaced unilateral facet fracture which was managed nonoperatively. Several demographic variables and clinical outcomes were recorded. Using computed tomography scanning and plain radiographs, fracture pattern, listhesis, displacement, angle and percentage of the facet that included the fracture were determined. Radiographic progression was defined as the occurrence of listhesis of more than 10% of the anterior-posterior dimensions of the inferior vertebral body during radiographic follow-up. Failure of conservative management was defined as a patient requiring surgical intervention after initially being managed nonoperatively. Results: Seventy-four patients were included. Fifteen patients (20%) progressed radiographically. However, only 2 developed radicular symptoms and none developed myelopathy or other catastrophic cord related symptoms. Seven patients (9%) underwent surgery. Indications for surgery included significant radiographic progression and/or radicular symptoms. Risk factors for failure of conservative management included presence of radiculopathy at the time of presentation, a higher body mass index, increased Injury Severity Score, greater initial fracture displacement and more than 2 mm of listhesis. Conclusions: Patients with non-displaced or minimally displaced facet fractures who do not have neurological symptoms at the time of presentation can safely be managed conservatively with careful observation and follow-up.

Factors influencing plant regeneration from seedling explants of Hairy nightshade (Solanum sarrachoides)

Ju, Ho-Jong,Van Eck, Joyce,Gray, Stewart M. Springer-Verlag 2012 Plant cell, tissue and organ culture Vol.108 No.1

Optimization of AFLP Fingerprinting of Organisms with a Large Genome size

Tae-Ho Han(한태호),Herman van Eck,Marjo de Jeu 한국원예학회 2001 한국원예학회 학술발표요지 Vol.2001 No.5

RNAi-mediated silencing of endogenous Vlnv gene confers stable reduction of cold-induced sweetening in potato (Solanum tuberosum L. cv. Désirée)

Amir Hameed,Rakhshanda Bilal,Farooq Latif,Joyce Van Eck,Georg Jander,Shahid Mansoor 한국식물생명공학회 2018 Plant biotechnology reports Vol.12 No.3

Potato tubers must be cold-stored to extend their shelf life and maintain an uninterrupted supply chain for food processors. However, a side-effect of low-temperature storage is manifested in terms of cold-induced sweetening (CIS) of potato tubers, which reduces the processing quality and the commercial value of the end-products. RNA interference (RNAi) technology, whereby transgene-derived small interfering RNAs can trigger the homology-based knockdown of cognate host genes and can initiate gene silencing, has been successfully applied in crop improvement through targeted gene knockout in host plants. In the current study, transgenic potato plants (Solanum tuberosum cv. Désirée) were generated, expressing a 300 bp hairpin loop nucleotide sequence targeting the potato vacuolar invertase gene (VInv), under the constitutive Cauliflower mosaic virus 35S promoter. Tubers collected from transgenic lines showed a significant reduction in reducing sugar content after 180 days of cold storage, without showing any measurable off-target effects on plant morphology and tuberization compared to nontransformed control plants. The cold-stored tubers were further assayed for chip color, which showed a fairly light colored quality in the samples originating from RNAi lines. Together with similar effects seen in previously published experiments involving other potato varieties, the Désirée results described here establish the efficacy of using RNAi for the successful reduction of CIS in potato tubers.

Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators

Xu, Cao,Park, Soon Ju,Van Eck, Joyce,Lippman, Zachary B. Cold Spring Harbor Laboratory 2016 Genes & development Vol.30 No.18

<P>Plant productivity depends on inflorescences, flower-bearing shoots that originate from the stem cell populations of shoot meristems. Inflorescence architecture determines flower production, which can vary dramatically both between and within species. In tomato plants, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF), but the underlying mechanism is unknown. We show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB (Broad complex, Tramtrack, and Bric-a-brac)/POZ (POX virus and zinc finger) domain. TMF and three tomato BOPs (S1BOPs) interact with themselves and each other, and TMF recruits S1BOPs to the nucleus, suggesting formation of a transcriptional complex. Like TMF, S1BOP gene expression is highest during vegetative and transitional stages of meristem maturation, and CRISPR/Cas9 elimination of S1BOP function causes pleiotropic defects, most notably simplification of inflorescences into single flowers, resembling tmf mutants. Flowering defects are enhanced in higher-order s1bop tmf mutants, suggesting that S1BOPs function with additional factors. In support of this, S1BOPs interact with TMF homologs, mutations in which cause phenotypes like sibop mutants. Our findings reveal a new flowering module defined by S1BOP TMF family interactions that ensures a progressive meristem maturation to promote inflorescence complexity.</P>

Scavenger Receptor BI Deficiency in Mice Is Associated With Plasma Ceramide and Sphingomyelin Accumulation and a Reduced Cholesteryl Ester Fatty Acid Length and Unsaturation Degree

Menno Hoekstra,Zhengzheng Zhang,Peter W. Lindenburg,Miranda Van Eck 한국지질동맥경화학회 2024 지질·동맥경화학회지 Vol.13 No.1

ObjectiveScavenger receptor class B type I (SR-BI) is primarily known for its role in the selective uptake of cholesteryl esters (CEs) from high-density lipoproteins (HDLs). Here we investigated whether SR-BI deficiency is associated with other potentially relevant changes in the plasma lipidome than the established effect of HDL-cholesterol elevation. MethodsTargeted ultra-high-performance liquid chromatography-tandem mass spectrometry was utilized to measure lipid species in plasma from female wild-type and SR-BI knockout mice. ResultsSR-BI deficiency was associated with a reduction in the average CE fatty acid length (−2%; p<0.001) and degree of CE fatty acid unsaturation (−18%; p<0.001) due to a relative shift from longer, polyunsaturated CE species CE (20:4), CE (20:5), and CE (22:6) towards the mono-unsaturated CE (18:1) species. Sphingomyelin (SM) levels were 64% higher (p<0.001) in SR-BI knockout mice without a parallel change in (lyso)phosphatidylcholine (LPC) concentrations, resulting in an increase in the SM/LPC ratio from 0.102±0.005 to 0.163±0.003 (p<0.001). In addition, lower LPC lengths (−5%; p<0.05) and fatty acid unsaturation degrees (−20%; p<0.01) were detected in SR-BI knockout mice. Furthermore, SR-BI deficiency was associated with a 4.7-fold increase (p<0.001) in total plasma ceramide (Cer) levels, with a marked >9-fold rise (p<0.001) in Cer (d18:1/24:1) concentrations. ConclusionWe have shown that SR-BI deficiency in mice not only impacts the CE concentrations, length, and saturation index within the plasma compartment, but is also associated with plasma accumulation of several Cer and SM species that may contribute to the development of specific hematological and metabolic (disease) phenotypes previously detected in SR-BI knockout mice.

Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato

Soyk, Sebastian,Mü,ller, Niels A,Park, Soon Ju,Schmalenbach, Inga,Jiang, Ke,Hayama, Ryosuke,Zhang, Lei,Van Eck, Joyce,Jimé,nez-Gó,mez, José,M,Lippman, Zachary B Nature Publishing Group, a division of Macmillan P 2017 Nature genetics Vol.49 No.1

<P>Plants evolved so that their flowering is triggered by seasonal changes in day lengths. However, day-length sensitivity in crops limits their geographical range of cultivation, and thus modification of the photoperiod response was critical for their domestication(2-11). Here we show that loss of day-length-sensitive flowering in tomato was driven by the florigen paralog and flowering repressor SELF-PRUNING 5G (SP5G). SP5G expression is induced to high levels during long days in wild species, but not in cultivated tomato because of cis-regulatory variation. CRISPR/Cas9-engineered mutations in SP5G cause rapid flowering and enhance the compact determinate growth habit of field tomatoes, resulting in a quick burst of flower production that translates to an early yield. Our findings suggest that pre-existing variation in SP5G facilitated the expansion of cultivated tomato beyond its origin near the equator in South America, and they provide a compelling demonstration of the power of gene editing to rapidly improve yield traits in crop breeding.</P>

Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene

Soyk, Sebastian,Lemmon, Zachary H.,Oved, Matan,Fisher, Josef,Liberatore, Katie L.,Park, Soon Ju,Goren, Anna,Jiang, Ke,Ramos, Alexis,van der Knaap, Esther,Van Eck, Joyce,Zamir, Dani,Eshed, Yuval,Lippma Cell Press 2017 Cell Vol. No.

<P><B>Summary</B></P> <P>Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing “jointless” fruit stems that reduced fruit dropping and facilitated mechanical harvesting. Stacking both beneficial traits caused undesirable branching and sterility due to epistasis, which breeders overcame with suppressors. However, this suppression restricted the opportunity for productivity gains from weak branching. Exploiting natural and engineered alleles for multiple family members, we achieved a continuum of inflorescence complexity that allowed breeding of higher-yielding hybrids. Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms.</P> <P><B>Video Abstract</B></P> <P>Display Omitted</P> <P><B>Highlights</B></P> <P> <UL> <LI> Mutations in two MADS-box genes were selected in tomato domestication and breeding </LI> <LI> Interaction of the alleles caused extreme inflorescence branching and sterility </LI> <LI> Natural and gene-edited MADS-box alleles provide a range of inflorescence types </LI> <LI> Dosage from selected alleles allows improved inflorescence architecture and yield </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>