Article
Multidisciplinary Sciences
Veronica Gonzalez-Pena, Sivaraman Natarajan, Yuntao Xia, David Klein, Robert Carter, Yakun Pang, Bridget Shaner, Kavya Annu, Daniel Putnam, Wenan Chen, Jon Connelly, Shondra Pruett-Miller, Xiang Chen, John Easton, Charles Gawad
Summary: Primary template-directed amplification (PTA) is an isothermal whole genome amplification method that accurately captures over 95% of single cell genomes, improving variant detection sensitivity and precision. By utilizing PTA, studies such as direct measurement of environmental mutagenicity (DMEM) and genome-wide off-target detection post CRISPR-mediated editing in single cells become feasible. PTA overcomes the current limitations of accurate WGA, enabling research on genetic diversity and evolution at cellular resolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
O. Y. Olivia Tse, Peiyong Jiang, Suk Hang Cheng, Wenlei Peng, Huimin Shang, John Wong, Stephen L. Chan, Liona C. Y. Poon, Tak Y. Leung, K. C. Allen Chan, Rossa W. K. Chiu, Y. M. Dennis Lo
Summary: The study developed a methodology for direct detection of S-Methylcytosine, achieving genome-wide SmC detection at single-base resolution in various biological samples with high sensitivity and specificity. It also allowed for the measurement of allele-specific methylation patterns in imprinted genes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Lena Goshayeshi, Sara Yousefi Taemeh, Nima Dehdilani, Mohammadreza Nasiri, Mohammad M. Ghahramani Seno, Hesam Dehghani
Summary: The study demonstrates the use of an RNA-guided piggyBac transposase and dual sgRNAs for site-directed integrations in the human ROSA26 safe harbor region. This methodology shows promise for targeting specific genomic regions, such as in cancer cells for inserting sequences into target regions or activating tumor suppressor genes.
Article
Biochemical Research Methods
Zhiqiang Yan, Jianting An, Yong Peng, Siming Kong, Qiang Liu, Ming Yang, Qilong He, Shi Song, Yidong Chen, Wei Chen, Rong Li, Jie Qiao, Liying Yan
Summary: Transcriptomic and epigenetic alterations in early embryo development are essential for regulating cell fate, with advances in single-cell techniques providing valuable data. However, the lack of integrated data collection and unified analytics hinders their application in research and clinical settings, necessitating the establishment of a database for human and mouse early embryo regulatory information. DevOmics is introduced as a tool for researchers to study molecular mechanisms in early embryos.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biology
Konstantina Athanasopoulou, Glykeria N. Daneva, Michaela A. Boti, Georgios Dimitroulis, Panagiotis G. Adamopoulos, Andreas Scorilas
Summary: Deciphering the etiopathogenesis of cancer is a complex task that requires a multidimensional approach. The introduction of next- and third-generation sequencing technologies has provided powerful tools for cancer research and has expanded the scope of personalized cancer medicine and pharmacogenomics.
Article
Biochemistry & Molecular Biology
Christopher Riccardi, Iacopo Passeri, Lisa Cangioli, Camilla Fagorzi, Marco Fondi, Alessio Mengoni
Summary: DNA methylation is a commonly observed epigenetic modification found in both eukaryotes and prokaryotes, and it is implicated in various biological phenomena such as gene regulation and adaptation to the environment. Advances in third-generation sequencing technologies have enabled the direct detection of genome-wide methylation profiles, providing opportunities to understand and utilize the epigenomic landscape at the individual and population levels. Here, we introduce a pipeline called MeStudio, which analyzes and combines genome-wide methylation profiles with genomic features, allowing for the identification of DNA methylation in coding and noncoding sequences. We demonstrate the utility and performance of MeStudio using single-molecule real-time sequencing outputs from Sinorhizobium meliloti strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yi Liu, Qing Chen, Jian-Zheng Yang, Xiu-Wen Li, Li-Jian Chen, Kai-Kai Zhang, Jia-Li Liu, Jia-Hao Li, Clare Hsu, Long Chen, Jia-Hao Zeng, Qi Wang, Dong Zhao, Jing-Tao Xu, Bernard Lebleu, Celestino Sardu
Summary: In this study, a mouse model of Takotsubo syndrome (TTS) was established to investigate the role of the sigma-1 receptor (Sigmar1) in TTS development. It was found that Sigmar1 knockout exacerbated cardiac dysfunction and led to dysregulation of the gut microbiome, tryptophan metabolism, and several signaling pathways, which play important roles in TTS pathogenesis. These findings provide valuable insights into the function of Sigmar1 in TTS and suggest that it may be a promising therapeutic target.
Article
Gastroenterology & Hepatology
Kathie A. Mihindukulasuriya, Ruben A. T. Mars, Abigail J. Johnson, Tonya Ward, Sambhawa Priya, Heather R. Lekatz, Krishna R. Kalari, Lindsay Droit, Tenghao Zheng, Ran Blekhman, Mauro D'Amato, Gianrico Farrugia, Dan Knights, Scott A. Handley, Purna C. Kashyap
Summary: The gut virome is stable over time but varies among subsets of patients with IBS. Specific changes in phage populations were identified in different IBS subsets, and they were correlated with bacterial composition and diet.
Review
Biochemistry & Molecular Biology
Annamaria Tisi, Sakthimala Palaniappan, Mauro Maccarrone
Summary: This article presents the application of advanced omics techniques, such as genomics, transcriptomics, and epigenomics, in cochlear research. The article also introduces the latest technologies, including single-cell omics and spatial omics, for investigating molecular events at a single-cell resolution with spatial information.
Article
Biochemistry & Molecular Biology
Fan Zhou, Biaodi Liu, Xin Liu, Yan Li, Luoluo Wang, Jia Huang, Guanzheng Luo, Xiaoyun Wang
Summary: This study investigated the impact of microbiome and microbiota-derived sodium butyrate on host transcriptome and metabolome using Drosophila model. The results demonstrated that sodium butyrate can influence host gene expression patterns and gut bacterial structures, with lipids being the dominant changed components in Drosophila metabolites. The integrative analysis of multi-omics data identified candidate transcripts coregulated by sodium butyrate, enhancing the understanding of host-microbiome interactions at a molecular level.
Article
Agriculture, Dairy & Animal Science
Mang Liang, Bingxing An, Tianpeng Chang, Tianyu Deng, Lili Du, Keanning Li, Sheng Cao, Yueying Du, Lingyang Xu, Lupei Zhang, Xue Gao, Junya Li, Huijiang Gao
Summary: Genomic selection (GS) has revolutionized animal and plant breeding. In this study, a model was built using the Cosine kernel to map genomic and transcriptomic data as matrices and combined with the best linear unbiased prediction (BLUP) method. Five kernel-based prediction models were defined and evaluated in a Chinese Simmental beef cattle population. The results showed that the inclusion of transcriptome data in GS improved the accuracy, and the weighted multi-omics single-step BLUP (wmssBLUP) and multi-omics single-step BLUP (mssBLUP) had higher prediction accuracy compared to genomic BLUP (GBLUP). Furthermore, the accuracy of wmssBLUP increased with the proportion of transcribed cattle.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Carolina D. Alberca, Ligia A. Papale, Andy Madrid, Reid S. Alisch
Summary: Whole genome methylation profiling reveals the systemic contributions of DNA methylation to ASD, with shared differentially methylated regions (DMRs) between brain and blood tissues. These regions are linked to risk genes for neurodevelopmental disorders and intellectual disabilities, suggesting the influence of DNA methylation on gene expression regulation in ASD pathogenesis.
HUMAN MOLECULAR GENETICS
(2023)
Article
Genetics & Heredity
Nandan P. Deshpande, Stephen M. Riordan, Claire J. Gorman, Shaun Nielsen, Tonia L. Russell, Carolina Correa-Ospina, Bentotage S. M. Fernando, Shafagh A. Waters, Natalia Castano-Rodriguez, Si Ming Man, Nicodemus Tedla, Marc R. Wilkins, Nadeem O. Kaakoush
Summary: This study comprehensively assessed the esophageal microenvironment in patients with gastro-esophageal reflux disease and metaplasia, identifying bacterial strain-specific signatures with high relevance to disease progression.
Article
Biotechnology & Applied Microbiology
Adam Nunn, Christian Otto, Mario Fasold, Peter F. Stadler, David Langenberger
Summary: This study presents a computational pre-processing approach to enable downstream analysis on a per-strand basis using conventional variant calling software. The method improves precision and sensitivity compared to specialized tools, and is applicable to both human and model plant variants.
Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Bala Ani Akpinar, Tugdem Muslu, Gadi V. P. Reddy, Munevver Dogramaci, Hikmet Budak
Summary: This article examines long noncoding RNAs (lncRNAs), a type of noncoding RNA that is typically over 200 nucleotides in length but lacks coding potential. Through analyzing two different wheat varieties, potential lncRNAs were identified, and potential functional networks with microRNAs were observed. Additionally, lncRNAs with perfect or near-perfect matches to organellar genomes were discovered.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Plant Sciences
Mohd Fadhli Hamdan, Goetz Hensel, Anshu Alok, Boon Chin Tan
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Anna Sazanova, Andrey Belimov, Yuri Gogolev, Elizaveta Chirak, Alexey Afonin, Denis Karlov, Irina Kuznetsova, Polina Guro, Lyudmila Kuzmina, Vera Safronova
Summary: In this article, we report the complete genome sequences of Massilia sp. strains B-10 (RCAM05335) and H-1 (RCAM05339), which were isolated from the water of the Dal'nee Verkhnee Lake in the Shulgan-Tash cave in Russia (53 degrees 2 ' 0 '' N, 57 degrees 3 ' 0 '' E). The sequences were obtained using an Oxford Nanopore Technologies MinION system.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biochemistry & Molecular Biology
Julia Shumilina, Alexey S. Kiryushkin, Nadezhda Frolova, Valeria Mashkina, Elena L. Ilina, Vera A. Puchkova, Katerina Danko, Svetlana Silinskaya, Evgeny B. Serebryakov, Alena Soboleva, Tatiana Bilova, Anastasia Orlova, Elizaveta D. Guseva, Egor Repkin, Katharina Pawlowski, Andrej Frolov, Kirill N. Demchenko
Summary: The main role of RALF small signaling peptides is to control the alkalization of the apoplast for nutrient absorption improvement. However, the specific function of individual RALF peptides such as RALF34 is still unknown. In this study, we used cucumber transgenic hairy roots overexpressing CsRALF34 to investigate its role in the regulatory pathway. The results showed that CsRALF34 overexpression inhibited root growth and regulated cell proliferation, specifically blocking the G2/M transition in cucumber roots. We propose that CsRALF34 modulates ROS homeostasis and triggers controlled production of hydroxyl radicals, possibly associated with intracellular signal transduction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alexey S. Kiryushkin, Elena L. Ilina, Elizaveta D. Guseva, Katharina Pawlowski, Kirill N. Demchenko
Summary: This study aimed to understand the signaling induced by RALF34 in cucumber. The expression of CsRALF34 was observed in all plant organs, and unlike AtRALF34, its expression was not regulated by auxin. CsTHESEUS1 showed constitutive expression in cucumber root tissues. The results suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Volodymyr Radchuk, Zeinu M. Belew, Andre Guendel, Simon Mayer, Alexander Hilo, Goetz Hensel, Rajiv Sharma, Kerstin Neumann, Stefan Ortleb, Steffen Wagner, Aleksandra Muszynska, Christoph Crocoll, Deyang Xu, Iris Hoffie, Jochen Kumlehn, Joerg Fuchs, Fritz F. Peleke, Jedrzej J. Szymanski, Hardy Rolletschek, Hussam H. Nour-Eldin, Ljudmilla Borisjuk
Summary: This study focuses on the functionality of the SWEET family of barley and reveals the crucial role of HvSWEET11b in the distribution of sugars and cytokinins during grain development. Knocking down HvSWEET11b leads to impaired grain development, disrupted sugar and cytokinin distribution, and changes in grain size, starch content, and protein content. The findings highlight the important regulatory role of HvSWEET11b in barley grain filling.
Article
Forestry
Soledad Ovando-Mena, Freddy Mora-Poblete, Romulo Santelices-Moya, Carlos Palacios-Rojas, Antonio M. Cabrera-Ariza
Summary: The primary objective of this study was to determine the spatial distribution pattern of N. alessandrii and its association with geomorphometric variables. The results showed that N. alessandrii trees had a random distribution pattern and a significant spatial association with the studied geomorphometric variables.
Article
Food Science & Technology
Elena V. V. Tyutereva, Anna A. A. Dalinova, Kirill N. N. Demchenko, Valeriya A. A. Dmitrieva, Vsevolod R. R. Dubovik, Yuriy V. V. Lukinskiy, Galina V. V. Mitina, Olga V. V. Voitsekhovskaja, Alexander Berestetskiy
Summary: This study investigated the effects of two ten-membered lactones on different plants and found that these toxins caused leaf damage, decreased pigment content, and electrolyte leakage. Additionally, these compounds also affected mitochondrial membrane potential and cell division. The results of this study revealed the mechanisms of action of these phytotoxic macrolides.
Article
Multidisciplinary Sciences
Yongyu Huang, Roop Kamal, Nandhakumar Shanmugaraj, Twan Rutten, Venkatasubbu Thirulogachandar, Shuangshuang Zhao, Iris Hoffie, Goetz Hensel, Jeyaraman Rajaraman, Yudelsy Antonia Tandron Moya, Mohammad-Reza Hajirezaei, Axel Himmelbach, Naser Poursarebani, Udda Lundqvist, Jochen Kumlehn, Nils Stein, Nicolaus von Wiren, Martin Mascher, Michael Melzer, Thorsten Schnurbusch
Summary: Flowering plants with indeterminate inflorescences often produce more floral structures than necessary. In barley (Hordeum vulgare L.), the initiation and maturation of floral primordia are molecularly decoupled. Initiation is primarily controlled by flowering-time genes, while floral growth is regulated by barley CCT MOTIF FAMILY 4 (HvCMF4) through light signaling, chloroplast, and vascular developmental programs. Mutations in HvCMF4 result in increased primordia death and pollination failure due to reduced rachis greening and limited energy supply to floral tissues. HvCMF4 is proposed to be a light sensory factor that coordinates floral initiation and survival with the vascular-localized circadian clock. Notably, stacking beneficial alleles for primordia number and survival has positive implications for grain production. These findings offer insights into the molecular mechanisms of grain number determination in cereal crops.
Article
Plant Sciences
Talles de Oliveira Santos, Antonio Teixeira do Amaral Jr, Rosimeire Barboza Bispo, Wallace de Paula Bernado, Bruna Rohem Simao, Valter Jario de Lima, Marta Simone Mendonca Freitas, Freddy Mora-Poblete, Roberto dos Santos Trindade, Samuel Henrique Kamphorst, Weverton Pereira Rodrigues, Eliemar Campostrini, Flavia Nicacio Viana, Cosme Damiao Cruz
Summary: Nitrogen is essential for plant growth, and improving nitrogen use efficiency is crucial for sustainable agriculture. This study found that heterosis had significant effects on growth traits and nitrogen use efficiency in popcorn, especially under low nitrogen conditions. Exploring heterosis is an effective strategy for obtaining superior hybrids and promoting nitrogen utilization, which is relevant and beneficial for sustainable agricultural practices and improved crop productivity.
Article
Biochemistry & Molecular Biology
Sunny Ahmar, Karolina Zolkiewicz, Damian Gruszka
Summary: Plant Glycogen Synthase Kinases (GSKs) play a crucial role in regulating various physiological processes by enabling crosstalk among signaling pathways. However, the mechanisms that regulate the expression of GSK genes during plant development and stress responses are still largely unknown. This study provides a detailed analysis of GSK promoters in rice and Arabidopsis, as well as characterization of expression profiles under different conditions. The results offer valuable insights into the regulatory mechanisms and may serve as a reference for future research in other plant species.
Editorial Material
Biochemistry & Molecular Biology
Sunny Ahmar, Damian Gruszka
Summary: This study reports a new strategy to create high-yielding, semi-dwarf wheat varieties with improved nitrogen-use efficiency by inhibiting brassinosteroid signaling through CRISPR/Cas9-mediated knockout of the ZnF-B gene encoding a zinc-finger RING-type E3 ligase.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Plant Sciences
Gesa Helmsorig, Agatha Walla, Thea Ruetjes, Gabriele Buchmann, Rebekka Schueller, Goetz Hensel, Maria von Korff
Summary: The eam7 locus in barley controls photoperiodic flowering by modifying the diurnal expression pattern of the major photoperiod response gene Ppd-H1.
Review
Biotechnology & Applied Microbiology
Sunny Ahmar, Goetz Hensel, Damian Gruszka
Summary: Cereal crops play a significant role in human consumption and animal feed, but face challenges from climate change and population expansion. Gene-editing technologies, such as CRISPR/Cas9, offer a potential solution to develop stress-tolerant and high-yielding cereal varieties. However, there are challenges to overcome, including time-consuming processes, limited genotypes for transformation, and restrictive regulations on genetically modified organisms (GMOs).
BIOTECHNOLOGY ADVANCES
(2023)