Article
Plant Sciences
Hongyan Yin, Yu Yan, Wei Hu, Guoyin Liu, Hongqiu Zeng, Yunxie Wei, Haitao Shi
Summary: This study identified specific SNPs affecting ionomic variation in cassava through genome-wide association studies, with some SNPs associated with both calcium and magnesium. Many loci for different ionomic traits appear to be clustered on specific chromosome regions. The study also found peak SNPs in promoter regions of genes related to nitrogen and phosphorus accumulation, positively modulating nutrient levels in cassava.
Article
Biology
Harsh Vashistha, Maryam Kohram, Hanna Salman
Summary: The heterogeneity of cells within an isogenic population is influenced by stochasticity in intracellular biochemical processes and resource distribution during divisions, but is limited by the inheritance of cellular components between generations. A new experimental method has been introduced to measure proliferation of heterogeneity in bacterial cell characteristics by tracking the differentiation between sister cells over time. Inherited dynamics of cellular properties and the long-term memory of cells to maintain these properties reveal mechanisms of non-genetic inheritance in bacteria and how cells control properties and heterogeneity within isogenic populations.
Article
Multidisciplinary Sciences
William B. Reinar, Anne Greulich, Ida M. Sto, Jonfinn B. Knutsen, Trond Reitan, Ole K. Torresen, Sissel Jentoft, Melinka A. Butenko, Kjetill S. Jakobsen
Summary: Intrinsically disordered protein regions play a crucial role in plant responses to biotic and abiotic stresses. Length variations in tracts of identical amino acids in these regions are influenced by natural selection and correlate with local bioclimatic habitat. Experimental evidence shows that length variations in a disordered transcription factor affect protein function and may have adaptive significance. Understanding the role of length variations in modulating protein function has implications for protein evolution and eco-evolutionary biology.
Article
Multidisciplinary Sciences
Fengju Chen, Yiqun Zhang, Darshan S. Chandrashekar, Sooryanarayana Varambally, Chad J. Creighton
Summary: This study combines mass spectrometry-based proteomics data with whole genome sequencing data to investigate the impact of non-coding somatic mutations on protein expression in cancer. The results show that about 25% of genes with SV-associated cis-regulatory alterations at the mRNA level are also associated at the protein level. SVs associated with enhancer hijacking, retrotransposon translocation, altered DNA methylation, or fusion transcripts are implicated in protein over-expression. These findings provide insights into the importance of non-coding somatic mutations in tumors.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Lu Shi, Jing Su, Myeong-Je Cho, Hao Song, Xiaoou Dong, Ying Liang, Zhiyong Zhang
Summary: Gene expression plays a crucial role in crop plant regulation. Genome editing of plant promoters offers the potential to modify gene expression patterns and create favorable traits. This can be done by precise generation of nucleotide sequences or by generating random mutations in the promoter region to select elite alleles based on phenotypic effects.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Medicine, General & Internal
Lorena Carrascal-Laso, Maria Isidoro-Garcia, Ignacio Ramos-Gallego, Manuel A. Franco-Martin
Summary: Current research has summarized the influence of different CYP450 gene polymorphisms on the metabolism of second-generation antipsychotic drugs, particularly olanzapine, clozapine, aripiprazole, risperidone, and quetiapine. Although significant differences in pharmacokinetic parameters between different phenotypes have been observed, more comprehensive studies describing pharmacokinetic interactions and environmental conditions among other variables are needed to fully understand these pharmacogenetic interactions.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Biology
Melanie N. Brien, Juan Enciso-Romero, Victoria J. Lloyd, Emma V. Curran, Andrew J. Parnell, Carlos Morochz, Patricio A. Salazar, Pasi Rastas, Thomas Zinn, Nicola J. Nadeau
Summary: Iridescent structural color in butterflies has a complex genetic basis, with variations in genes and scale ultrastructure playing important roles in color formation. Different species show differences in the relationship between structure and color.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Nicolaas C. Budhiparama, Imelda Lumban-Gaol, Herawati Sudoyo, Rahadyan Magetsari, Tri Wibawa
Summary: This study aimed to evaluate the association of SNPs of the IL-1 family with the clinical severity of knee OA. Three SNPs of IL-1R1, rs871659, rs3771202, and rs3917238, were associated with primary knee OA. No correlation was found between SNPs of IL-1R1 and IL-1RN and clinical or radiologic severity or serum concentrations of IL-1R1 and IL-1Ra. BMI and IL-1R1 rs3917238 genotype C/C were correlated with moderate-severe VAS scores.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Shixian Hu, Werna T. Uniken Venema, Harm-Jan Westra, Arnau Vich Vila, Ruggero Barbieri, Michiel D. Voskuil, Tjasso Blokzijl, Bernadien H. Jansen, Yanni Li, Mark J. Daly, Ramnik J. Xavier, Gerard Dijkstra, Eleonora A. Festen, Rinse K. Weersma
Summary: The study investigated intestinal biopsies from 171 IBD patients and identified inflammation-dependent intestinal cis-eQTLs that mainly interact with prevalence of immune cell types. This genetic susceptibility under inflammatory conditions may guide future drug development and precision medicine in IBD patients.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Multidisciplinary
Xiaoqiang Yin, Yangyang Li, Jingwen Zhou, Shengqi Rao, Guocheng Du, Jian Chen, Song Liu
Summary: This study utilized random mutagenesis and site-directed genetic modification to enhance the production of TGase in Streptomyces mobaraensis. A mutant (smY2019) with a 5.5-fold increase in TGase yield was successfully screened, and two additional TGase expression cassettes were integrated into its genome, resulting in a recombinant strain (smY2019-3C) with a 103% increase in TGase production compared to smY2019. The smY2019-3C strain with 40 U/mL of TGase yield could be a suitable candidate for industrial production of TGase.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Andrew M. Scott, Janice L. Yan, Carling M. Baxter, Ian Dworkin, Reuven Dukas
Summary: Male sexual aggression towards females is a complex behavior influenced by both genetic and environmental factors. In this study, researchers used fruit flies as a model system to investigate the genetic contributions to variation in forced copulations (FCs). They found that hundreds of genes were associated with evolved and plastic variation in FC, but only a small proportion showed consistent differential expression in both modes of variation. Functional analysis revealed the enrichment of genes related to neuropeptide hormone activity and serotonin receptor activity. Knockdown experiments confirmed the role of four genes in FC behavior. Overall, this study provides valuable insights into the genetic architecture underlying natural variation in sexual aggression.
Article
Plant Sciences
Walaa M. R. M. Adly, Gniewko Niedbala, Mohammad E. EL-Denary, Mahasen A. Mohamed, Magdalena Piekutowska, Tomasz Wojciechowski, El-Sayed T. Abd El-Salam, Ahmed S. Fouad
Summary: This study aimed to create potato somaclones with an improved potential for starch accumulation. Through the upregulation of six starch-synthesis-related genes, the somaclonal variant Ros 119 exhibited increased starch content and enhanced tuberization potential compared to the parent cv Lady Rosetta. This somaclonal variant provides a valuable resource for potato breeding programs.
Article
Multidisciplinary Sciences
Xueyang Dong, Ben G. H. Guthrie, Margaret Alexander, Cecilia Noecker, Lorenzo Ramirez, Nathaniel R. Glasser, Peter J. Turnbaugh, Emily P. Balskus
Summary: This study develops genetic tools for the direct manipulation of Eggerthella lenta and other Coriobacteriia, including shuttle vectors, transformation methods, and genome editing systems. Using these tools, the researchers characterize endogenous promoters and inducible expression systems in Eggerthella lenta, and uncover a novel family of transcriptional regulators in gut Coriobacteriia. Furthermore, they utilize these genetic tools to study the effects of Eggerthella lenta genes on host biology.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Asli Azizoglu, Roger Brent, Fabian Rudolf
Summary: The study introduces a new gene expression controller, WTC846, for precise and graded gene expression in Saccharomyces cerevisiae, independent of growth conditions. This controller allows for adjustable protein expression across a range of cellular abundances with limited variation.
Article
Immunology
Melvin Zhang, Jennifer L. Duffen, Karl H. Nocka, Marion T. Kasaian
Summary: IL-13 regulates the activity of IL-33 by modulating the transmembrane and soluble forms of ST2, impacting the responsiveness to IL-33. IL-13-deficient mice showed exacerbated effects following IL-33 administration, highlighting the important regulatory role of IL-13 on IL-33.
JOURNAL OF IMMUNOLOGY
(2021)
Editorial Material
Gastroenterology & Hepatology
Y. U. S. U. K. E. Shimakawa, G. I. B. R. I. L. Ndow, A. T. S. U. S. H. Kaneko, K. A. T. S. U. M. Aoyagi, M. A. U. D. Lemoine, Y. A. S. U. H. I. T. O. Tanaka
CLINICAL GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Oncology
Michihiro Yoshida, Hiroshi Yukawa, Kazuki Hayashi, Itaru Naitoh, Katsuyuki Miyabe, Yasuki Hori, Makoto Natsume, Naruomi Jinno, Akihisa Kato, Kenta Kachi, Go Asano, Hidenori Sahashi, Tadashi Toyohara, Kayoko Kuno, Yusuke Kito, Hiromu Kondo, Atsuyuki Hirano, Fumihiro Okumura, Kaiki Anbe, Yoshinobu Baba, Hiromi Kataoka, Yasuhito Tanaka
Summary: This study investigates the potential biomarkers for biliary tract cancers (BTCs) through the analysis of exosomal microRNAs (miRNAs) in bile samples. The results suggest that several exosomal miRNAs in bile show aberrant expression, while no abnormal expression is found in serum samples. MiR-451a and miR-3619-3p are identified as reproducible upregulated markers in bile, and their combination can effectively diagnose BTCs.
Article
Gastroenterology & Hepatology
Korenobu Hayama, Masanori Atsukawa, Akihito Tsubota, Chisa Kondo, Motoh Iwasa, Hiroshi Hasegawa, Koichi Takaguchi, Akemi Tsutsui, Haruki Uojima, Hisashi Hidaka, Hironao Okubo, Tatsuya Suzuki, Kentaro Matsuura, Toshifumi Tada, Naoto Kawabe, Joji Tani, Asahiro Morishita, Toru Ishikawa, Yoshitaka Arase, Yoshihiro Furuichi, Keizo Kato, Kazuhito Kawata, Makoto Chuma, Akito Nozaki, Atsushi Hiraoka, Tsunamasa Watanabe, Tatehiro Kagawa, Hidenori Toyoda, Nobuhiko Taniai, Hiroshi Yoshida, Yasuhito Tanaka, Katsuhiko Iwakiri
Summary: This study aimed to evaluate the outcome in patients with portal vein thrombosis (PVT) who received antithrombin III-based therapy. The results showed that maintenance therapy, favorable response, and absence of PVT progression may suppress or control liver-related events in antithrombin III-based therapy for PVT patients.
HEPATOLOGY RESEARCH
(2023)
Editorial Material
Gastroenterology & Hepatology
Kotaro Waki, Kenshi Matsuno, Hideaki Miyamoto, Ryosuke Gushima, Hiroki Takeda, Yorihisa Orita, Yasuhito Tanaka
Article
Biochemistry & Molecular Biology
Go Sugahara, Yuji Ishida, Jae Jin Lee, Meng Li, Yasuhito Tanaka, Hyungjin Eoh, Yusuke Higuchi, Takeshi Saito
Summary: This study aimed to define the environmental requirements necessary for maintaining the homeostasis of terminally differentiated hepatocytes. The supplementation of dimethyl sulfoxide (DMSO) was found to be indispensable for mitigating fate deterioration and promoting adaptation to the in vitro environment. Dimethyl sulfone (DMSO2) was identified as a substitute for DMSO, supporting the long-term maintenance of hepatocyte morphology, marker gene expression, and functionality.
Article
Gastroenterology & Hepatology
Harry L. A. Janssen, Jinlin Hou, Tarik Asselah, Henry L. Y. Chan, Fabien Zoulim, Yasuhito Tanaka, Ewa Janczewska, Ronald G. Nahass, Stefan Bourgeois, Maria Buti, Pietro Lampertico, Oliver Lenz, Thierry Verbinnen, Joris Vandenbossche, Willem Talloen, Ronald Kalmeijer, Maria Beumont, Michael Biermer, Umesh Shukla
Summary: The study evaluated the efficacy and safety of JNJ-56136379 in patients with chronic hepatitis B. The results showed that JNJ-56136379+NA significantly reduced HBV DNA and HBV RNA levels, but had limited effects on HBsAg or HBeAg declines in HBeAg-positive patients. Overall, JNJ-56136379 did not demonstrate clear superiority over NA in terms of efficacy.
Article
Gastroenterology & Hepatology
Masanori Atsukawa, Akihito Tsubota, Chisa Kondo, Kaori-Shioda Koyano, Toru Ishikawa, Hidenori Toyoda, Koichi Takaguchi, Tsunamasa Watanabe, Kentaro Matsuura, Chikara Ogawa, Atsushi Hiraoka, Hironao Okubo, Masakuni Tateyama, Haruki Uojima, Akito Nozaki, Makoto Chuma, Keizo Kato, Shigeru Mikami, Joji Tani, Asahiro Morishita, Kazuhito Kawata, Toshifumi Tada, Yoshihiro Furuichi, Tomomi Okubo, Tadamichi Kawano, Taeang Arai, Naoto Kawabe, Naohiro Kawamura, Tadashi Ikegami, Makoto Nakamuta, Ryuta Shigefuku, Motoh Iwasa, Yasuhito Tanaka, Masaru Hatano, Katsuhiko Iwakiri
Summary: This study identified factors associated with a high TRPG in cirrhosis patients and developed a scoring model to identify those at high risk of PoPH, which can be used to select patients who may benefit from echocardiography investigations.
HEPATOLOGY INTERNATIONAL
(2023)
Article
Gastroenterology & Hepatology
Daniel Q. Huang, Andrew Tran, Ming-Lun Yeh, Satoshi Yasuda, Pei-Chien Tsai, Chung-Feng Huang, Chia Yen Dai, Eiichi Ogawa, Masatoshi Ishigami, Takanori Ito, Ritsuzo Kozuka, Masaru Enomoto, Takanori Suzuki, Yoko Yoshimaru, Carmen M. Preda, Raluca I. Marin, Irina Sandra, Sally Tran, Sabrina X. Z. Quek, Htet Htet Toe Wai Khine, Norio Itokawa, Masanori Atsukawa, Haruki Uojima, Tsunamasa Watanabe, Hirokazu Takahashi, Kaori Inoue, Mayumi Maeda, Joseph K. Hoang, Lindsey Trinh, Scott Barnett, Ramsey Cheung, Seng Gee Lim, Huy N. Trinh, Wan-Long Chuang, Yasuhito Tanaka, Hidenori Toyoda, Ming-Lung Yu, Mindie H. Nguyen
Summary: This study aimed to evaluate the association between antiviral therapy and the risk of hepatocellular carcinoma (HCC) in patients with indeterminate-phase chronic hepatitis B (CHB). The analysis of 855 treatment-naive CHB patients showed that antiviral therapy reduced the risk of developing HCC.
Article
Virology
Danny Ka-Ho Wong, Takako Inoue, Lung-Yi Mak, Rex Wan-Hin Hui, James Fung, Ka-Shing Cheung, Wai-Kay Seto, Yasuhito Tanaka, Man-Fung Yuen
Summary: This study evaluated the usefulness of two novel assays, the iTACT-HBsAg and iTACT-HBcrAg assays, in CHB patients with HBsAg seroclearance (SC). The results showed that over 70% of patients still had a low level of HBV protein expression even at 10 years after SC, indicating that CHB patients with SC still harbor a low level of HBV. Further investigations are needed to determine the clinical significance of detectable viral proteins after SC.
JOURNAL OF CLINICAL VIROLOGY
(2023)
Article
Gastroenterology & Hepatology
Tatsuki Mizuochi, Itaru Iwama, Ayano Inui, Yoshinori Ito, Yugo Takaki, Sotaro Mushiake, Daisuke Tokuhara, Takashi Ishige, Koichi Ito, Jun Murakami, Haruka Hishiki, Hitoshi Mikami, Kazuhiko Bessho, Ken Kato, Ryosuke Yasuda, Yushiro Yamashita, Yasuhito Tanaka, Hitoshi Tajiri
Summary: This study assessed the real-world efficacy and safety of glecaprevir and pibrentasvir (G/P) treatment in Japanese adolescents with chronic hepatitis C virus (HCV). The results showed that G/P treatment was highly efficacious and well tolerated, with all patients achieving sustained virologic response at 12 weeks after treatment completion.
JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Oncology
Takayuki Tokunaga, Masakuni Tateyama, Yasuteru Kondo, Satoshi Miuma, Shiho Miyase, Kentaro Tanaka, Satoshi Narahara, Hiroki Inada, Sotaro Kurano, Yoko Yoshimaru, Katsuya Nagaoka, Takehisa Watanabe, Hiroko Setoyama, Kotaro Fukubayashi, Motohiko Tanaka, Yasuhito Tanaka
Summary: This study aimed to evaluate the impact of therapeutic modifications of atezolizumab plus bevacizumab therapy in patients with unresectable hepatocellular carcinoma (uHCC). Patients with therapeutic modifications other than discontinuation of both drugs had favorable overall survival and time to progression, while those with discontinuation of both drugs had unfavorable outcomes. Modified liver function and immune-related adverse events increased the risk of discontinuation without other therapeutic modifications. Avoiding discontinuation without other therapeutic modifications may be the optimal management for uHCC.
Article
Medicine, Research & Experimental
Takeshi Chida, Yuji Ishida, Sho Morioka, Go Sugahara, Christine Han, Bill Lam, Chihiro Yamasaki, Remi Sugahara, Meng Li, Yasuhito Tanaka, T. Jake Liang, Chise Tateno, Takeshi Saito
Summary: Hepatitis delta virus (HDV), a satellite virus of HBV, induces a potent and persistent activation of the IFN system in human hepatocytes, while HBV is not capable of triggering a hepatic antiviral response. HDV's constitutive activation of the hepatic IFN system suppresses HBV but modestly inhibits HDV, creating a paradoxical mode of viral interference. Furthermore, the study reveals that HDV-induced constitutive IFN system activation leads to IFN refractoriness, rendering therapeutic IFNs ineffective.
Article
Gastroenterology & Hepatology
Hiroko Setoyama, Nao Nishida, Shintaro Nagashima, Ko Ko, Taiji Yamazoe, Yasuhito Tanaka, Masashi Mizokami, Junko Tanaka, Tatsuya Kanto
Summary: This study aimed to establish a reliable host genome analysis technique for countries with inadequate infrastructure, and found associations between HLA-DPB1 and hepatitis B in the Cambodian population.
HEPATOLOGY RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Hiroki Kumamoto, Nobuyo Higashi-Kuwata, Sanae Hayashi, Debananda Das, Haydar Bulut, Ryoh Tokuda, Shuhei Imoto, Kengo Onitsuka, Yuka Honda, Yuki Odanaka, Satoko Shimbara-Matsubayashi, Kazuhiro Haraguchi, Yasuhito Tanaka, Hiroaki Mitsuya
Summary: Encouraged by previous findings, we designed and synthesized compound 6 as a hybrid of potent anti-HBV agents 4 and 5. The stereospecific construction of the chiral quaternary carbon portion was achieved through radical-mediated cyclization. The introduction of a fluorine atom was accomplished through stannylation and electrophilic fluorination. Compound (E)-6 displayed highly potent anti-HBV activity and favorable cytotoxicity.
Article
Gastroenterology & Hepatology
Kenshi Matsuno, Hideaki Miyamoto, Hideki Kitada, Shinichi Yoshimatsu, Fumio Tamura, Kouichi Sakurai, Kotaro Fukubayashi, Takashi Shono, Hiroko Setoyama, Taichi Matsuyama, Shinichiro Suko, Rei Narita, Munenori Honda, Masakuni Tateyama, Hideaki Naoe, Jun Morinaga, Yasuhito Tanaka, Ryosuke Gushima
Summary: This study compared the efficacy of endoscopic submucosal resection with band ligation (ESMR-L) and endoscopic submucosal dissection (ESD) in the treatment of small rectal neuroendocrine tumors (NETs). The results showed that both methods had similar high complete resection rates, but ESMR-L had shorter procedure time and hospitalization period, making it a more efficient treatment method, especially for less-experienced endoscopists.