Article
Biochemical Research Methods
Martin Lycka, Vratislav Peska, Martin Demko, Ioannis Spyroglou, Agata Kilar, Jiri Fajkus, Miloslava Fojtova
Summary: This study introduces a new online toolset called WALTER for the rapid, reproducible, and user-friendly analysis of telomere length data and statistical evaluation, representing a major upgrade in TRF scan image processing.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Itty Sethi, Gh. Rasool Bhat, Rakesh Kumar, Ekta Rai, Swarkar Sharma
Summary: Telomeres, highly repetitive regions at chromosome ends, are challenging to quantify due to their complex structure. A cost-effective qPCR method utilizing a dual labeled fluorescence probe has been developed to improve accuracy in telomere length measurement.
Article
Biochemistry & Molecular Biology
Maha Sellami, Shamma Al-muraikhy, Hend Al-Jaber, Hadaia Al-Amri, Layla Al-Mansoori, Nayef A. Mazloum, Francesco Donati, Francesco Botre, Mohamed A. Elrayess
Summary: This study found that levels of TNF-α were significantly higher in older athletes, while IL-10 significantly increased in high-intensity endurance sports regardless of age group, and IL-6 concentration was higher in older athletes participating in high-intensity sports. Overall, significant positive correlations were identified among levels of IL-6, IL-10, IL-8, and TNF-α.
Article
Nutrition & Dietetics
Amelia Marti, Maria Fernandez de la Puente, Silvia Canudas, Guillermo Zalba, Cristina Razquin, Cristina Valle-Hita, Montse Fito, Miguel Angel Martinez-Gonzalez, Sonia Garcia-Calzon, Jordi Salas-Salvado
Summary: This study aimed to identify environmental and lifestyle factors that could slow down telomere shortening in order to prevent chronic diseases. The results showed that a three-year intervention based on an energy-reduced Mediterranean diet and physical activity could slow down telomere shortening in women, but not in men.
CLINICAL NUTRITION
(2023)
Article
Public, Environmental & Occupational Health
Daniel Nettle, Shahinaz M. Gadalla, Tsung-Po Lai, Ezra Susser, Melissa Bateson, Abraham Aviv
Summary: Researchers are increasingly interested in testing hypotheses about the impact of environmental or disease exposures on telomere length through longitudinal study designs. While telomere length is usually measured with qPCR in population studies, differences in measurement error exist. Findings indicate that longitudinal analysis provides a greater statistical power gain for SB method compared to qPCR.
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Daniel Nettle, Shahinaz M. Gadalla, Tsung-Po Lai, Ezra Susser, Melissa Bateson, Abraham Aviv
Summary: Research indicates that longitudinal study designs are more effective than cross-sectional studies in testing the impact of environmental or disease exposures on telomere length, reducing measurement errors. Results demonstrate that SB has greater statistical power than qPCR when measuring telomere length changes.
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Oncology
Jagannath Pal, Yogita Rajput, Shruti Shrivastava, Renuka Gahine, Varsha Mungutwar, Tripti Barardiya, Ankur Chandrakar, Pinaka Pani Ramakrishna, Sovna Shivani Mishra, Hansa Banjara, Vivek Choudhary, Pradeep K. Patra, Masood A. Shammas
Summary: Oral squamous cell carcinoma (OSCC) is often preceded by a white patch called oral leukoplakia (OL). Telomere length (TL) measurement has potential as a predictive biomarker in OL, but its translational application is limited due to variability and lack of a universal reference. This study introduces an approach of evaluating TL using paired peripheral blood mononuclear cells (PBMC) as an internal reference, which eliminates the need for external reference DNA and provides a useful marker to define high-risk OL groups.
MOLECULAR ONCOLOGY
(2022)
Article
Microbiology
Cheng-Hung Lai, Yu-Sin Lin, Chao-Min Wang, Poa-Chun Chang, Wei-Yau Shia
Summary: This study identified Capnocytophaga strains in the oral cavity of dogs using 16S rRNA and phylogenetic analysis. A novel 16S rRNA PCR-RFLP method was designed to accurately distinguish C. cynodegmi from C. canimorsus, improving detection accuracy. This method is important for the epidemiological study of Capnocytophaga and the rapid diagnosis of human C. canimorsus infections following exposure to small animals.
MICROBIOLOGY SPECTRUM
(2023)
Article
Construction & Building Technology
Michael Bekele Maru, Yusen Wang, Hansun Kim, Hyungchul Yoon, Seunghee Park
Summary: The AEC industry can benefit from accurate building facade segmentation, and LiDAR sensors combined with an empirical-based intensity correction model can help achieve this. The proposed method utilizes a deep learning model to classify building facade components and incorporates digital twin technology for real-time segmentation and generating valuable insights about the building.
JOURNAL OF BUILDING ENGINEERING
(2023)
Article
Engineering, Electrical & Electronic
Feng Wang, Ying Sun, Qiang Chen, Jingjing Xing, Yihua Xia, Yixin Zhang, Xuping Zhang
Summary: In this paper, a method is proposed to correct the nonlinear frequency sweep in optical frequency domain reflectometry (OFDR) by introducing an acousto-optic modulator as the frequency shifter. Experimental results demonstrate that this method can improve the spatial resolutions and robustness for different correction methods, showing a wide-range effect in the promotion of OFDR technique.
JOURNAL OF LIGHTWAVE TECHNOLOGY
(2022)
Article
Entomology
Zhi-Chao Yan, Hai-Qing Hua, Guang-Yuan Qi, Yuan-Xi Li
Summary: We developed a method to detect and identify Trichogramma larvae in their host eggs and successfully differentiated eight Trichogramma species using a PCR-RFLP assay. This study provides a promising approach for conveniently identifying Trichogramma in insectaries and accurately evaluating parasitism rates in the field.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2022)
Article
Obstetrics & Gynecology
Rao Gurugubelli Krishna, Ballambattu Vishnu Bhat, Zachariah Bobby, Dasari Papa, Bhawana Badhe, Palanivel Chinnakali
Summary: The study found that genomic DNA methylation was significantly lower in IUGR neonates compared to AGA neonates, but there was no significant difference in telomere length between the two groups.
JOURNAL OF MATERNAL-FETAL & NEONATAL MEDICINE
(2021)
Article
Plant Sciences
Harleen Kaur, Jhulia Gelain, Marcus Vinicius Marin, Natalia A. Peres, Guido Schnabel
Summary: A new Neopestalotiopsis sp. has been discovered in strawberry plants in Florida, Georgia, and South Carolina, causing severe leaf spot and fruit rot. This new species is more aggressive and destructive than other Pestalotiopsis pathogens, leading to significant yield losses for affected growers. The study developed a molecular method based on PCR/RFLP for accurate and fast identification of the new Neopestalotiopsis sp. variant from strawberry plants. This method utilizes PCR amplification of a beta-tubulin gene fragment and the restriction enzyme BsaWI to differentiate the new species from others.
Article
Automation & Control Systems
Yinhui Xie, Jinxing Yang, Weilong Huang, Jun Li
Summary: This paper proposes a new tool-path planning method based on improved Prim algorithm for CCOS techniques. Simulation and experimental results show that this method can shorten path length, increase polishing efficiency, and improve texture and mid-frequency errors.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2022)
Article
Plant Sciences
Jenna T. B. Ekwealor, Simone D. Benjamin, Jordan Z. Jomsky, Matthew A. Bowker, Lloyd R. Stark, D. Nicholas McLetchie, Brent D. Mishler, Kirsten M. Fisher
Summary: This study presents a technique to determine the genotypic sex of S. caninervis moss and examines the genotypic and phenotypic sex ratios in a case study. The results show that the genotypic ratio of non-expressing shoots is female-biased and exceeds the phenotypic ratio. Additionally, the distribution of male and female genotypes is not predicted by sex expression patterns in different microhabitats.
APPLICATIONS IN PLANT SCIENCES
(2022)
Article
Multidisciplinary Sciences
Janett Goehring, Florian Kellner, Lukas Schrangl, Rene Platzer, Enrico Klotzsch, Hannes Stockinger, Johannes B. Huppa, Gerhard J. Schuetz
Summary: This study introduces a FRET-based sensor that directly measures the magnitude and kinetics of forces imposed by TCR at the single molecule level. Results showed that when T cells were confronted with gel-phase SLBs, there was a single force peak of around 5pN prior and upon activation, with force loading rates around 1.5pN per second on the TCR; while facing fluid-phase SLBs, T cells exerted tensile forces prior to activation but not afterwards, although of reduced magnitude compared to gel-phase SLBs.
NATURE COMMUNICATIONS
(2021)
Article
Optics
B. Buchegger, A. Haghofer, D. Hoeglinger, J. Jacak, S. Winkler, A. Hochreiner
Summary: Shaping the optical wavefront with spatial light modulators is valuable for focal spot modification, and has applications in multiphoton lithography focus optimization. A low-cost approach using a Raspberry Pi camera was used for feedback, and images of the focal spot were input for an evolutionary algorithm to improve focus quality.
OPTICS AND LASERS IN ENGINEERING
(2021)
Article
Biochemical Research Methods
Fabian Hauser, Jaroslaw Jacak
Summary: The algorithm presented in this study allows real-time analysis of 3D single molecule localization microscopy images with minimal impact on fitting accuracy, utilizing lookup-tables with discrete xyz-positions. Real-time visualization during acquisition is achieved, with performance demonstrated on both simulated and measured data. Furthermore, a feedback loop controlling the activation laser pulse maintains a constant number of emitters per image frame.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Genetics & Heredity
J. Matthew Watson, Johanna Trieb, Martina Troestl, Kyle Renfrew, Terezie Mandakova, Jaroslav Fulnecek, Dorothy E. Shippen, Karel Riha
Summary: The study demonstrates that telomeres of 400 bp are necessary and sufficient for Arabidopsis viability, with longer telomeres promoting telomerase processivity or recruitment. The findings suggest that telomeres long enough to form a t-loop constitute the minimal functional length.
Article
Biochemistry & Molecular Biology
Mariana Romeiro Motta, Xin'Ai Zhao, Martine Pastuglia, Katia Belcram, Farshad Roodbarkelari, Maki Komaki, Hirofumi Harashima, Shinichiro Komaki, Manoj Kumar, Petra Bulankova, Maren Heese, Karel Riha, David Bouchez, Arp Schnittger
Summary: Flowering plants contain multiple cyclin families, with B1-type cyclins playing a crucial role in cell cycle control during Arabidopsis development. Mutant analysis revealed complex overlapping requirements of B1-type cyclins, with CYCB1;2 being central. The double mutant cycb1;1 cycb1;2, although compromised in growth, provides a unique opportunity to study the function of B1-type cyclins at the organismic level.
Article
Biochemistry & Molecular Biology
Karin Strohmeier, Martina Hofmann, Fabian Hauser, Dmitry Sivun, Sujitha Puthukodan, Andreas Karner, Georg Sandner, Pol-Edern Le Renard, Jaroslaw Jacak, Mario Mairhofer
Summary: Research found that EVs modified with CRISPR/Cas9 technology have a higher proportion of single-GFP-labeled particles compared to conventionally over-expressed EVs. This approach can reduce bias caused by over-expression, and the modified EVs can be accurately detected and distinguished in cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Lukas Schrangl, Janett Goehring, Florian Kellner, Johannes B. Huppa, Gerhard J. Schuetz
Summary: Single-molecule Forster resonance energy transfer (smFRET) is a versatile technique used to report distances in the sub-nanometer to nanometer range, widely applied in biophysical and molecular biological experiments. By combining single-molecule tracking with alternating excitation (ALEX) smFRET experiments, surface-bound but mobile probes in plasma membranes or glass-supported lipid bilayers can be studied.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Cell Biology
Eleni Priglinger, Juergen Strasser, Boris Buchroithner, Florian Weber, Susanne Wolbank, Daniela Auer, Eva Grasmann, Claudia Arzt, Dmitry Sivun, Johannes Grillari, Jaroslaw Jacak, Johannes Preiner, Mario Gimona
Summary: Interest in using mesenchymal stem cell derived extracellular vesicles (MSC-EVs) as therapeutic agents has grown in the past decade. This study established and verified quartz crystal microbalance (QCM) as a highly sensitive label-free immunosensing technique for characterizing clinically approved umbilical cord MSC-EVs. By using QCM along with common characterization methods, specific detection of EVs via EV and MSC markers was achieved, allowing for quantitative determination of the ratio of marker-specific EVs versus non-vesicular particles.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Article
Multidisciplinary Sciences
Albert Cairo, Anna Vargova, Neha Shukla, Claudio Capitao, Pavlina Mikulkova, Sona Valuchova, Jana Pecinkova, Petra Bulankova, Karel Riha
Summary: In Arabidopsis, the transition from meiosis to mitosis is driven by translation inhibition involving processing bodies. The meiosis-specific protein TDM1 is incorporated into processing bodies through interaction with SMG7, sequestering the main translation initiation complex and inhibiting translation. Chemical inhibition of translation can overcome the failure to terminate meiosis in tdm1 mutants. TDM1-containing processing bodies down-regulate meiotic transcripts to facilitate the transition of cell fates.
Review
Biochemistry & Molecular Biology
Vivek K. Raxwal, Karel Riha
Summary: NMD is a conserved quality control pathway that inhibits the expression of transcripts containing premature termination codon. It plays important roles in regulating gene expression and various physiological processes in plants.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Immunology
Alexandra van der Staal, Janett Goehring, Anna Ohradanova-Repic, Markus Kramer, Clemens Donner, Andreas Zech, Marco Idzko, Hannes Stockinger
Summary: Interstitial lung disease poses challenges for diagnosis due to complex pathophysiological mechanisms, overlapping conditions, and interobserver disagreement. We developed a patient clustering model based on surface phenotyping of immune cells and clinical data to offer an additional approach in complex cases. Our model allows for rapid identification of divergent profiles within a diagnostic group and removes physician bias by relying on cellular nearest neighbors for sample clustering.
IMMUNOLOGY LETTERS
(2023)
Article
Plant Sciences
Sorin Tanasa, Neha Shukla, Albert Cairo, Ranjani S. Ganji, Pavlina Mikulkova, Sona Valuchova, Vivek K. Raxwal, Claudio Capitao, Arp Schnittger, Zbynek Zdrahal, Karel Riha
Summary: Meiosis is a specialized cell division that reduces the number of chromosomes, followed by mitotic divisions to form haploid gametophytes in angiosperm plants. In Arabidopsis, the termination of meiosis and transition to gametophytic development are regulated by TDM1 and SMG7, which inhibit translation. Mutants deficient in this mechanism show aberrant nuclear divisions due to the failure to downregulate cyclin dependent kinases during meiotic exit. A mutation in cyclin-dependent kinase D;3 (CDKD;3) was identified as a suppressor that alleviates meiotic defects in smg7 deficient plants by preventing aberrant meiotic divisions or delaying their onset. CDKD;3 acts independently of CDKA;1 and interacts with proteins involved in cytokinesis, suggesting a complex role in cell cycle regulation.
Meeting Abstract
Biophysics
Bianca Buchegger, Alexander Tanzer, Christian Gabriel, Thomas A. Klar, Jaroslaw Jacak
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Meeting Abstract
Biophysics
Fabian Hauser, Eleni Priglinger, Sandra Milic, Boris Buchroithner, Christoph Naderer, Jaroslaw Jacak
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
