Explanipedia

Elucidation of new sulfamethoxazole catabolic pathways in whole-cell catalyst of bacterium Kocuria rhizophila SA117 Open

Tomáš Řezanka, Jiří Zahradník, Sofía G. Zavala-Meneses, Helena Marešová, Michal Řezanka , et al. · 2025

Sulfamethoxazole (SMX) and its residues exhibit high environmental persistence due to their resistance to conventional degradation processes. The bacterial strain Kocuria rhizophila SA117, isolated from polluted soils, was characterized bi…

In Vitro and Viral Evolution Convergence Reveal the Selective Pressures Driving Omicron Emergence Open

Aviv Shoshany, R. Tian, M. Blanco, A. Sen Hruska, Aditi Konar , et al. · 2025

In vitro protein evolution provides powerful insights into the amino acid sequences that underlie key biological functions. Here, we used this approach to explore the evolutionary trajectories of the SARS-CoV-2 spike protein receptor-bindi…

Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1 Open

Hisano Yajima, Yuki Anraku, Yu Kaku, Kanako Kimura, Arnon Plianchaisuk , et al. · 2024

Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants Open

Hisano Yajima, Tomo Nomai, Kaho Okumura, Katsumi Maenaka, Jumpei Ito , et al. · 2024

Due to the incessant emergence of various SARS-CoV-2 variants with enhanced fitness in the human population, controlling the COVID-19 pandemic has been challenging. Understanding how the virus enhances its fitness during a pandemic could o…

Variant-proof high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways Open

Matthew Gagné, Barbara J. Flynn, Christopher Cole Honeycutt, Dillon R. Flebbe, Shayne F. Andrew , et al. · 2024

Virological characteristics of the SARS‐CoV‐2 Omicron EG.5.1 variant Open

Shuhei Tsujino, Sayaka Deguchi, Tomo Nomai, Miguel Padilla‐Blanco, Arnon Plianchaisuk , et al. · 2024

In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phy…

Virological characteristics of the SARS-CoV-2 BA.2.86 variant Open

Tomokazu Tamura, Keita Mizuma, Hesham Nasser, Sayaka Deguchi, Miguel Padilla‐Blanco , et al. · 2024

In late 2023, several SARS-CoV-2 XBB descendants, notably EG.5.1, were predominant worldwide. However, a distinct SARS-CoV-2 lineage, the BA.2.86 variant, also emerged. BA.2.86 is phylogenetically distinct from other Omicron sublineages, a…

Virological characteristics of the SARS-CoV-2 JN.1 variant Open

Yu Kaku, Kaho Okumura, Miguel Padilla‐Blanco, Yusuke Kosugi, Keiya Uriu , et al. · 2024

Characterization of the evolutionary and virological aspects of mutations in the receptor binding motif of the SARS-CoV-2 spike protein Open

Yuuka Masuda, Hesham Nasser, Jiří Zahradník, Shuya Mitoma, Ryo Shimizu , et al. · 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has substantially diversified during the pandemic, resulting in the successive emergence of variants characterized by various mutations. It has been observed that several epidemi…

Virological characteristics of the SARS-CoV-2 JN.1 variant Open

Yu Kaku, Kaho Okumura, Miguel Padilla‐Blanco, Yusuke Kosugi, Keiya Uriu , et al. · 2023

The SARS-CoV-2 BA.2.86 lineage, first identified in August 2023, is phylogenetically distinct from the currently circulating SARS-CoV-2 Omicron XBB lineages, including EG.5.1 and HK.3. Comparing to XBB and BA.2, BA.2.86 carries more than 3…

Virological characteristics of the SARS-CoV-2 BA.2.86 variant Open

Tomokazu Tamura, Keita Mizuma, Hesham Nasser, Sayaka Deguchi, Miguel Padilla‐Blanco , et al. · 2023

In late 2023, a lineage of SARS-CoV-2 emerged and was named the BA.2.86 variant. BA.2.86 is phylogenetically distinct from other Omicron sublineages identified so far, displaying an accumulation of over 30 amino acid mutations in its spike…

Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant Open

Shuhei Tsujino, Sayaka Deguchi, Tomo Nomai, Miguel Padilla‐Blanco, Arnon Plianchaisuk , et al. · 2023

In middle-late 2023, a sublineage of SARS-CoV-2 Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. Here, we performed multiscale investigations to reveal virological features of newly emerging EG.5.1 varia…

Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics Open

Izumi Kimura, Daichi Yamasoba, Hesham Nasser, Hayato Ito, Jiří Zahradník , et al. · 2023

Previous studies on the Omicron BA.2 variant suggested that the virological characteristics of BA.2 are determined by the mutations in at least two different regions of the viral genome: in the BA.2 spike gene (enhancing viral fusogenicity…

Datasets for the article "Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light" Open

Phuong Ngoc Pham, Jiří Zahradník, Gustavo Fuertes · 2023

The datasets include: - Circular dichroism (CD) spectra (Figure 3B). - Nano differential scanning fluorimetry (DSF) melting curves (Figure 3C). - Size-exclusion chromatography (SEC) elution profiles (Figure 3D). - Deconvoluted mass spectra…

Datasets for the article "Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light" Open

Phuong Ngoc Pham, Jiří Zahradník, Gustavo Fuertes · 2023

The datasets include: - Circular dichroism (CD) spectra (Figure 3B). - Nano differential scanning fluorimetry (DSF) melting curves (Figure 3C). - Size-exclusion chromatography (SEC) elution profiles (Figure 3D). - Deconvoluted mass spectra…

RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways Open

Matthew Gagné, Barbara J. Flynn, Christopher Cole Honeycutt, Dillon R. Flebbe, Shayne F. Andrew , et al. · 2023

SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the viru…

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants Open

Tomokazu Tamura, Jumpei Ito, Keiya Uriu, Jiří Zahradník, Izumi Kida , et al. · 2023

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant Open

Jumpei Ito, Rigel Suzuki, Keiya Uriu, Yukari Itakura, Jiří Zahradník , et al. · 2023

In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Her…

Engineering dynamic gates in binding pocket of penicillin G acylase to selectively degrade bacterial signaling molecules Open

Michal Grulich, Bartłomiej Surpeta, Andrea Palyzová, Helena Marešová, Jiří Zahradník , et al. · 2023

The rapid rise of antibiotic-resistant bacteria necessitates the search for alternative, unconventional solutions, such as targeting bacterial communication. Signal disruption can be achieved by enzymatic degradation of signaling compounds…

Virological characteristics of the SARS-CoV-2 omicron XBB.1.16 variant Open

Daichi Yamasoba, Keiya Uriu, Arnon Plianchaisuk, Yusuke Kosugi, Lin Pan , et al. · 2023

Virological characteristics of the SARS-CoV-2 Omicron XBB.1.16 variant Open

Daichi Yamasoba, Keiya Uriu, Arnon Plianchaisuk, Yusuke Kosugi, Lin Pan , et al. · 2023

At the end of March 2023, XBB.1.16, a SARS-CoV-2 omicron XBB subvariant, emerged and was detected in various countries. Compared to XBB.1.5, XBB.1.16 has two substitutions in the S protein: E180V is in the N-terminal domain, and T478R in t…

Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant Open

Keiya Uriu, Jumpei Ito, Jiří Zahradník, Shigeru Fujita, Yusuke Kosugi , et al. · 2023

Enhanced transmissibility, infectivity and immune resistance of the SARS-CoV-2 Omicron XBB.1.5 variant Open

Keiya Uriu, Jumpei Ito, Jiří Zahradník, Shigeru Fujita, Yusuke Kosugi , et al. · 2023

In 2022, we have elucidated the characteristics of a variety of newly emerging SARS-CoV-2 Omicron subvariants. At the end of 2022, the XBB.1.5 variant, an descendant of XBB.1 that acquired the S:F486P substitution, emerged and is rapidly s…

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants Open

Tomokazu Tamura, Jumpei Ito, Keiya Uriu, Jiří Zahradník, Izumi Kida , et al. · 2022

In late 2022, the SARS-CoV-2 Omicron subvariants have highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged by recombination of two co-circulating BA.2 lineages, BJ.1 and BM…

Convergent evolution of the SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant Open

Jumpei Ito, Rigel Suzuki, Keiya Uriu, Yukari Itakura, Jiří Zahradník , et al. · 2022

In late 2022, although the SARS-CoV-2 Omicron subvariants have highly diversified, some lineages have convergently acquired amino acid substitutions at five critical residues in the spike protein. Here, we illuminated the evolutionary rule…

The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant Open

Izumi Kimura, Daichi Yamasoba, Hesham Nasser, Jiří Zahradník, Yusuke Kosugi , et al. · 2022

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant Open

Akatsuki Saito, Tomokazu Tamura, Jiří Zahradník, Sayaka Deguchi, Koshiro Tabata , et al. · 2022

Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5 Open

Izumi Kimura, Daichi Yamasoba, Tomokazu Tamura, Naganori Nao, Tateki Suzuki , et al. · 2022

After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers o…

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 Open

Akatsuki Saito, Tomokazu Tamura, Jiří Zahradník, Sayaka Deguchi, Koshiro Tabata , et al. · 2022

SARS-CoV-2 Omicron BA.2.75 emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically different from BA.5, the currently predominant BA.2 descendant. Here, we showed that the effective reproduction number of BA.2.75 is great…

Genetically Engineered MRI-Trackable Extracellular Vesicles as SARS-CoV-2 Mimetics for Mapping ACE2 Binding <i>In Vivo</i> Open

Andrea Gálisová, Jiří Zahradník, Hyla Allouche‐Arnon, Mattia I. Morandi, Paula Abou Karam , et al. · 2022

The elucidation of viral-receptor interactions and an understanding of virus-spreading mechanisms are of great importance, particularly in the era of a pandemic. Indeed, advances in computational chemistry, synthetic biology, and protein e…

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