Article
Biochemical Research Methods
Chichi Dai, Pengmian Feng, Lizhen Cui, Ran Su, Wei Chen, Leyi Wei
Summary: The study developed a machine learning-based method (m(7)G-IFL) to identify m(7)G sites, extracting more discriminative features through the iterative feature learning process to improve predictive performance.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Hematology
James I. Hearn, Elizabeth E. Gardiner
Summary: This article discusses the role of platelets in the formation of a hemostatic response and vascular injury repair, as well as their function in flowing blood. The article highlights the importance of platelet adhesion and activation in forming and strengthening adhesive ties, and discusses the challenges faced in research.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Timothy Warwick, Sandra Seredinski, Nina M. Krause, Jasleen Kaur Bains, Lara Althaus, James A. Oo, Alessandro Bonetti, Anne Dueck, Stefan Engelhardt, Harald Schwalbe, Matthias S. Leisegang, Marcel H. Schulz, Ralf P. Brandes
Summary: This paper presents a new method for predicting RNA-DNA triple helix formation and develops the TriplexAligner program for predicting such interactions. The method predicts RNA-DNA interactions more accurately than previous methods in humans and mice and has been validated through biophysical experiments. This work is important for better understanding triplex formation and genome-wide analysis of RNA-DNA interactions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Chemistry, Multidisciplinary
Koji Hashimoto, Emil C. Fischer, Floyd E. Romesberg
Summary: The researchers have developed semisynthetic organisms that can store and retrieve increased information by using a series of synthetic, unnatural base pairs. Their results demonstrate that the E. coli RNA polymerase can transcribe DNA containing unnatural base pairs, and these advancements should facilitate the creation of next generation SSOs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Yinghui Feng, Qi Liu, Miao Chen, Xinyi Zhao, Lumin Wang, Longfei Liu, Xiaoqing Chen
Summary: In this study, a nucleic acid programmed strategy was used to develop nanocarriers that can precisely package multiple cargos, allowing for multiplexed analysis and comparison between normal individuals and patients with prostate enlargement. Additionally, the nanocarriers were also able to image and distinguish between different cancer cells and normal cells.
CHEMICAL COMMUNICATIONS
(2021)
Article
Cell Biology
Paul Vulliamy, Lucy Z. Kornblith, Matthew E. Kutcher, Mitchell J. Cohen, Karim Brohi, Matthew D. Neal
Summary: Platelets play a crucial role in the initial response to tissue injury, with altered responsiveness observed in both acutely injured patients and survivors. Aside from their role in coagulation, platelets contribute to the sterile inflammatory response to injury and can impact multiple-organ dysfunction syndromes.
Article
Biochemistry & Molecular Biology
Ankit K. Pathak, Gyan Prakash Mishra, Bharathram Uppili, Safal Walia, Saman Fatihi, Tahseen Abbas, Sofia Banu, Arup Ghosh, Amol Kanampalliwar, Atimukta Jha, Sana Fatma, Shifu Aggarwal, Mahesh Shanker Dhar, Robin Marwal, Venkatraman Srinivasan Radhakrishnan, Kalaiarasan Ponnusamy, Sandhya Kabra, Partha Rakshit, Rahul C. Bhoyar, Abhinav Jain, Mohit Kumar Divakar, Mohamed Imran, Mohammed Faruq, Divya Tej Sowpati, Lipi Thukral, Sunil K. Raghav, Mitali Mukerji
Summary: During the COVID-19 pandemic, genome sequencing of SARS-CoV-2 has been valuable for tracking its spread and identifying variants of concern. Intra-host single nucleotide variations (iSNVs) can capture variability within a host, and some variations have been found to become fixed in the population. Mutations in the Spike protein may affect antigenicity and immune escape. Therefore, tracking and studying iSNVs in ongoing genome surveillance programs is important for early identification of potential variants of concern.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Organic
Anna M. Rydzik, Regina Balk, Martin Koegler, Tobias Steinle, Doris Riether, Dirk Gottschling
Summary: In this study, a novel RNA phosphoramidite decorated with an amino functionality was synthesized and successfully incorporated into RNA oligonucleotides. The amino group could be further modified for various applications, indicating a potential vector for nucleobase replacements in RNA oligonucleotides.
Article
Cardiac & Cardiovascular Systems
Antoine Rauch, Annabelle Dupont, Mickael Rosa, Maximilien Desvages, Christina Le Tanno, Johan Abdoul, Melusine Didelot, Alexandre Ung, Richard Ruez, Emmanuelle Jeanpierre, Melanie Daniel, Delphine Corseaux, Hugues Spillemaeker, Julien Labreuche, Benedicte Pradines, Natacha Rousse, Peter J. Lenting, Mouhamed D. Moussa, Andre Vincentelli, Jean-Claude Bordet, Bart Staels, Flavien Vincent, Cecile V. Denis, Eric Van Belle, Caterina Casari, Sophie Susen
Summary: Thrombocytopenia is consistently observed in ECMO patients, with a time-dependent decrease in platelet count, GP Ib alpha shedding, and increased soluble GP Ib alpha levels. Shedding of GP Ib alpha is dependent on rheological conditions, with higher rates at high-flow speeds.
CIRCULATION RESEARCH
(2023)
Article
Biology
Shan Qi, Javier Mota, Siu-Hong Chan, Johanna Villarreal, Nan Dai, Shailee Arya, Robert A. Hromas, Manjeet K. Rao, Ivan R. Correa, Yogesh K. Gupta
Summary: The METTL3-METTL14 complex catalyzes methylation of RNA and DNA, with a preference for single-stranded DNA and structured RNA, respectively. The complex has a higher affinity for structured RNA but methylates RNA less efficiently than DNA. Furthermore, the methylation of DNA by the complex is restricted by structured RNA elements prevalent in cellular RNAs.
Article
Hematology
Alexander St. John, Yi Wang, Junmei Chen, Warren Osborn, Xu Wang, Esther Lim, Dominic Chung, Susan Stern, Nathan White, Xiaoyun Fu, Jose Lopez
Summary: This study describes the changes in plasma proteomic profile associated with platelet dysfunction after trauma, identifying twelve proteins with significant differences. The findings suggest that patients with platelet dysfunction are more severely injured but otherwise similar to those with retained platelet function.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2021)
Article
Electrochemistry
Bohuai Xiao, Yunchuan Li, Shuai Chang
Summary: This study demonstrates the successful detection and identification of four DNA nucleosides by introducing a cage-shaped molecule CB[7], and achieves accurate single base reading.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2022)
Review
Plant Sciences
Tania Chakraborty, Hayden Payne, Rebecca A. Mosher
Summary: The revolution in sequencing has provided a wealth of plant genomes for studying the evolution of biological complexity. Gene duplication drives complexity, and angiosperms encode various gene silencing pathways. Recent phylogenetic analysis reveals the expansion, specialization, and occasional contraction of these pathways.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Environmental Sciences
M. Hernandez-Garnica, J. D. Garcia-Garcia, R. Moreno-Sanchez, R. Sanchez-Thomas
Summary: The study analyzed the accumulation of lead by the free-living algae-like Euglena gracilis and its effects, revealing that the organism showed resistance to lead under certain conditions without significant changes in growth and photosynthesis.
ENVIRONMENTAL POLLUTION
(2021)
Article
Cell Biology
Yiming Feng, Yue Zhang, Jialan Shi
Summary: Classical myeloproliferative neoplasm (MPN) is a clonal disease characterized by abnormal expansion of hematopoietic stem cells. MPN patients are more susceptible to thrombotic events, but antiplatelet therapies may cause bleeding. Platelets play a critical role in the pathogenesis of MPN and optimizing antithrombotic treatment strategies by adjusting the administration of antiplatelet drugs may achieve simultaneous control of thrombosis and bleeding.
Article
Surgery
Annemarieke de Vlaming, Kyle G. Mathews, Jonathan A. Hash, Erin K. Keenihan, Samantha Sommer, Luke Borst, Shelly L. Vaden
Summary: Surgical options for maintaining continence after resection of trigono-urethral urothelial carcinoma (UC) are limited in canines. This study evaluated the creation of a continent urine reservoir solely vascularized by omentum and confirmed the feasibility of the procedure. Staged omentalization provided improved vascularity for the reservoir.
JOURNAL OF INVESTIGATIVE SURGERY
(2022)
Article
Engineering, Biomedical
He Shen, Bai Xu, Chao Yang, Weiwei Xue, Zhifeng You, Xianming Wu, Dezun Ma, Dan Shao, Kam Leong, Jianwu Dai
Summary: A dual-functional hydrogel scaffold was developed for treating SCI, scavenging DAMPs and releasing IL-10. In vitro and in vivo studies showed that this scaffold reduced proinflammatory responses, enhanced neurogenic differentiation, suppressed cytokine production, and promoted neural regeneration to a greater extent compared to control scaffolds.
Article
Multidisciplinary Sciences
Chengxin Shi, Jianati Dawulieti, Feiyu Shi, Chao Yang, Qian Qin, Tongfei Shi, Lizhao Wang, Hanze Hu, Madi Sun, Li Ren, Fangman Chen, Yawei Zhao, Feng Liu, Mingqiang Li, Lijun Mu, Dan Liu, Dan Shao, Kam W. Leong, Junjun She
Summary: A new nanomedicine strategy has been developed for the treatment of inflammatory bowel disease (IBD) by scavenging proinflammatory cell-free DNA and reactive oxygen species, with minimal side effects.
Article
Engineering, Biomedical
Yawen Ma, Huimin Lin, Peng Wang, Haocheng Yang, Jie Yu, Hao Tian, Tianyu Li, Shengfang Ge, Yilong Wang, Renbing Jia, Kam W. Leong, Jing Ruan
Summary: MicroRNA-based gene therapy using biocompatible nanocarriers shows promise in treating ocular melanoma by up-regulating tumor suppressor miR-30a-5p and inhibiting malignant phenotypes. The nanocarrier with high miRNA loading and redox-responsive release capabilities enhances the therapeutic effect. Furthermore, it promotes M1 macrophage polarization and activates Fenton reaction, synergistically enhancing anti-tumor immunity. The study demonstrates the potential of this nanocarrier for targeted gene therapy in melanoma and other cancers.
ACTA BIOMATERIALIA
(2023)
Article
Chemistry, Multidisciplinary
Jiaqi Xu, Junchao Xu, Tongfei Shi, Yinlong Zhang, Fangman Chen, Chao Yang, Xinjing Guo, Guangna Liu, Dan Shao, Kam W. Leong, Guangjun Nie
Summary: Microbiota-based therapeutics offer innovative strategies to treat inflammatory bowel diseases (IBDs), but the clinical outcome and bacterial approach need improvement. Inspired by the benefits of probiotics, bioartificial probiotics are designed to restore intestinal microenvironment and shift the gut microbiome to an anti-inflammatory state. The bioartificial probiotic consists of E. coli Nissle 1917-derived membrane (EM) as the surface and biodegradable diselenide-bridged mesoporous silica nanoparticles (SeM) as the core. This work suggests a safe and effective nanomedicine for IBDs therapy.
ADVANCED MATERIALS
(2023)
Article
Engineering, Biomedical
Baoding Huang, Qianfen Wan, Tianyu Li, Lexiang Yu, Wen Du, Carmen Calhoun, Kam W. Leong, Li Qiang
Summary: As a solution to the chronic inflammation and local adiposity caused by obesity, cationic polyamidoamine (PAMAM) treatment has shown promising results in improving metabolic functions and reducing body weight in diet-induced obese (DIO) mice. The treatment involves the use of PAMAM generation 3 (P-G3) scavenger and complexing P-G3 with human serum albumin (HSA) to achieve sustained release. Local injection of HSA-PG3 successfully restricts the distribution of the complex within the targeted adipose tissue and reduces focal adiposity.
Article
Cell & Tissue Engineering
Fei Fang, Yang Xiao, Elazar Zelzer, Kam W. Leong, Stavros Thomopoulos
Summary: This study used single-cell RNA sequencing to investigate the developmental transcriptome of mouse enthesis and identified six resident cell types, including Gli1-lineage cells, which have therapeutic potential for enthesis regeneration.
Article
Chemistry, Multidisciplinary
Naoto Yoshinaga, Joyce K. Zhou, Cong Xu, Chai Hoon Quek, Yuefei Zhu, Ding Tang, Lin Yung Hung, Sarah A. Najjar, Chin Ying Angela Shiu, Kara Gross Margolis, Yeh-Hsing Lao, Kam W. Leong
Summary: Effective delivery of CRISPR-Cas9 components is crucial and oral delivery has not been explored due to the degradative nature of the gastrointestinal tract. In this study, we developed novel PBA-functionalized CS-PEI polymers for oral CRISPR delivery, which showed effective penetration in the intestinal mucosa and achieved downregulation of the target protein and reduction in cholesterol. This study demonstrates the potential of addressing the needs of gene editing in a patient-compliant manner.
Article
Engineering, Biomedical
Ganchimeg Davaa, Jin Young Hong, Jung-Hwan Lee, Min Soo Kim, Jennifer O. Buitrago, Yu-Meng Li, Hae-Hyoung Lee, Dong Wook Han, Kam W. Leong, Jung Keun Hyun, Hae-Won Kim
Summary: Neural stem cells (NSC) have the potential to regenerate injured neural tissues, but suffer from low survival and uncontrolled differentiation. This study demonstrates that mechanically-tuned protein hydrogels can protect and enhance the long-term survival of reprogrammed NSC, alleviate neural inflammation, promote differentiation, and improve locomotor functions in treating injured spinal cord.
ADVANCED HEALTHCARE MATERIALS
(2023)
Article
Cell Biology
Yunfei Li, Zhixiong Sun, Huixiang Zhu, Yan Sun, David B. Shteyman, Sander Markx, Kam W. Leong, Bin Xu, Bingmei M. Fu
Summary: The integrity of the blood-brain barrier formed by brain microvascular endothelial cells derived from 22q11.2 Deletion Syndrome patients is compromised. The haploinsufficiency of CRKL, a gene within the 22q11.2 DS deletion region, contributes to this deficit. Treatment with imatinib, an FDA-approved drug, restores the compromised blood-brain barrier by increasing the level of active forms of the CRKL protein.
Article
Engineering, Biomedical
Hye Sung Kim, Tzu-Chieh Ho, Moshe J. Willner, Michael W. Becker, Hae-Won Kim, Kam W. Leong
Summary: In this study, we propose an ex vivo T cell expansion system that mimics natural antigen-presenting cells for adoptive cell therapy. The system utilizes microfiber scaffolds coated with dendritic cell membrane to replicate the physicochemical properties of dendritic cells, leading to greater expansion and functionality of T cells. This scalable and customizable platform holds promise for future research and application in cell therapy.
BIOACTIVE MATERIALS
(2023)
Article
Microbiology
Grayson K. Walker, Lyndy Harden, M. Mitsu Suyemoto, Siddhartha Thakur, Megan Jacob, Luke B. Borst
Summary: Coinfections by avian pathogenic Escherichia coli (APEC) and Enterococcus faecalis in poultry with colisepticemia are increasing. Here, we report draft genome sequences of 18 APEC and 18 E. faecalis strains coisolated from lesions of diseased poultry.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Veterinary Sciences
Rajdeep Multani, Eli B. Cohen, Jason Haas, Luke Borst, Mandy Womble, Sarah Musulin
Summary: This article reports a case of acute abdomen in a 7-month-old French bulldog, with ultrasound examination confirming pancreatic torsion.
JOURNAL OF THE AMERICAN ANIMAL HOSPITAL ASSOCIATION
(2023)
Article
Microbiology
Grayson K. Walker, Lyndy Harden, M. Mitsu Suyemoto, Siddhartha Thakur, Megan Jacob, Luke B. Borst
Summary: Escherichia coli and Enterococcus spp. are frequently found together in urine cultures of dogs with urinary tract infections. Enterococcus enhances uropathogenic E. coli in polymicrobial UTIs. We report the draft genome sequences of 12 UPEC co-isolated with Enterococcus spp. from canine urinary tract infections.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Chemistry, Multidisciplinary
Yongqiang Xiao, He Fang, Yuefei Zhu, Jie Zhou, Zhanzhan Dai, Hongxia Wang, Zhaofan Xia, Zhaoxu Tu, Kam W. Leong
Summary: This study investigates the effectiveness of cationic hyperbranched polyaminoglycosides derived from tobramycin (HPT) and disulfide-included HPT (ss-HPT) in scavenging cell-free nucleic acids (cfNAs) to mitigate posttrauma inflammation and hypercoagulation. Both polymers demonstrate the ability to suppress inflammation and hypercoagulation by efficiently scavenging cfNAs, and exhibit potent antibacterial effects. Additionally, these polymers exhibit favorable modulatory effects on inflammation and therapeutic outcomes in a mouse model. Notably, ss-HPT shows high accumulation and retention in injured organs of traumatized mice, with a higher biodegradation rate in healthy mice compared to HPT.