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1. Identification and up-regulation of three small heat shock proteins in summer and winter diapause in response to temperature stress in Pieris melete

Author:
Falak Naz Miano; Ting Jiang; Jing Zhang; Wan-Na Zhang; Yingchuan Peng; Hai-Jun Xiao
Source:
International journal of biological macromolecules 2022 v.209 pp. 1144-1154
ISSN:
0141-8130
Subject:
sequence alignment,   etc   ; diapause; heat stress; overwintering; phylogeny; summer; temperature;     Show all 7 Subjects
Abstract:
... Small heat shock proteins (sHSPs) are conserved proteins that play key roles in organismal adaptation to adversity stressors. However, little is known about sHSPs during summer diapause. Three sHSP genes: PmHSP19.5, PmHSP19.9, and PmHSP20.0 were identified and cloned from Pieris melete. Sequence alignment and phylogenetic analysis revealed that the three sHSPs have a typical, conserved α-crystalli ...
DOI:
10.1016/j.ijbiomac.2022.04.093

2. Tegumentary leishmaniasis by Leishmania braziliensis complex in Cochabamba, Bolivia including the presence of L. braziliensis outlier: Tegumentary leishmaniasis in Cochabamba, Bolivia: Tegumentary leishmaniasis in Cochabamba, Bolivia

Author:
Mary Cruz Torrico; Anna Fernández‐Arévalo; Cristina Ballart; Marco Solano; Ernesto Rojas; Eva Ariza; Silvia Tebar; Daniel Lozano; Alba Abras; Joaquim Gascón; Albert Picado; Carmen Muñoz; Faustino Torrico; Montserrat Gállego
Source:
Transboundary and emerging diseases 2022 v.69 no.4 pp. 2242-2255
ISSN:
1865-1674
Subject:
sequence alignment,   etc   ; Leishmania braziliensis; genes; genotype; leishmaniasis; patients; Bolivia;     Show all 7 Subjects
Abstract:
... Leishmaniasis is caused by protozoans of the Leishmania genus, which includes more than 20 species capable of infecting humans worldwide. In the Americas, the most widespread specie is L. braziliensis, present in 18 countries including Bolivia. The taxonomic position of the L. braziliensis complex has been a subject of controversy, complicated further by the recent identification of a particular s ...
DOI:
10.1111/tbed.14228

3. Functional analysis of a PISTILLATA-like gene CcMADS20 involved in floral organs specification in citrus

Author:
Xiao-Jin Hou; Li-Xia Ye; Xiao-Yan Ai; Chun-Gen Hu; Zhong-Ping Cheng; Jin-Zhi Zhang
Source:
Plant science 2022 v.319 pp. 111263
ISSN:
0168-9452
Subject:
sequence alignment,   etc   ; Arabidopsis; Citrus; phylogeny; transcription (genetics); transcription factors;     Show all 6 Subjects
Abstract:
... PISTILLATA (PI), as a member of MADS-box transcription factor, plays an important role in petal and stamen specification in Arabidopsis. However, little is known about PI-like genes in citrus. To understand the molecular mechanism of PI during the developmental process of citrus flower, a PI-like gene CcMADS20 was isolated from Citrus Clemantina. Sequence alignment and phylogenetic analysis reveal ...
DOI:
10.1016/j.plantsci.2022.111263

4. An Identification and Characterization of the Axolotl (Ambystoma mexicanum, Amex) Telomerase Reverse Transcriptase (Amex TERT)

Author:
Sina Springhetti; Vesna Bucan; Christina Liebsch; Andrea Lazaridis; Peter Maria Vogt; Sarah Strauß
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
sequence alignment,   etc   ; Ambystoma mexicanum; adults; genes; longevity; telomerase; telomeres;     Show all 7 Subjects
Abstract:
... The Mexican axolotl is one of the few vertebrates that is able to replace its lost body parts during lifespan. Due to its remarkable regenerative abilities, the axolotl emerged as a model organism especially for limb regeneration. Telomeres and the telomerase enzyme are crucial for regeneration and protection against aging processes and degenerating diseases. Despite its relevance for regeneration ...
DOI:
10.3390/genes13020373

5. Characterization of oxidosqualene cyclases from Trichosanthes cucumerina L. reveals key amino acids responsible for substrate specificity of isomultiflorenol synthase

Author:
Pornpatsorn Lertphadungkit; Xue Qiao; Min Ye; Somnuk Bunsupa
Source:
Planta 2022 v.256 no.3 pp. 58
ISSN:
0032-0935
Subject:
sequence alignment,   etc   ; Trichosanthes cucumerina; biosynthesis; lanosterol; metabolites; substrate specificity; transcriptome; triterpenoids;     Show all 8 Subjects
Abstract:
... MAIN CONCLUSION: Two key amino acids of isomultiflorenol synthase, Y125 and M254, were first proposed. They could be associated with the production of isomultiflorenol. Oxidosqualene cyclases (OSCs) are the first committed enzymes in the triterpenoid biosynthesis by converting 2,3-oxidosqualene to specific triterpenoid backbones. Thus, these enzymes are potential targets for developing plant-activ ...
DOI:
10.1007/s00425-022-03972-6

6. Crystal structure of 5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris presents multiple conformations

Author:
Tongtong Zhang; Jiuzhou Chen; Ping Zheng; Weimin Gong; Jibin Sun; Haiping Liu
Source:
Biochemical and biophysical research communications 2022 v.609 pp. 100-104
ISSN:
0006-291X
Subject:
sequence alignment,   etc   ; 5-aminolevulinate synthase; Rhodopseudomonas palustris; aminolevulinic acid; crystal structure; research;     Show all 6 Subjects
Abstract:
... 5-ALA is the precursor of all tetrapyrroles. 5-Aminolevulinate synthase (ALAS) catalyzes the production of 5-aminolevulinic acid (5-ALA) from glycine and succinyl-CoA. HemA from Rhodopseudomonas palustris (Rp-HemA) was reported to be a highly active ALAS. To understand the catalytic mechanism of Rp-HemA, the 2.05 Å resolution crystal structure of Rp-HemA was solved. Open, half close and close conf ...
DOI:
10.1016/j.bbrc.2022.04.021

7. Improved diagnostic and multiplex RT-qPCR for detecting rubella viral RNA

Author:
Min-Hsin Chen; Emily Abernathy; Joseph P. Icenogle; Ludmila M. Perelygina
Source:
Journal of virological methods 2022 v.306 pp. 114555
ISSN:
0166-0934
Subject:
sequence alignment,   etc   ; Rubella virus; blood serum; detection limit; genes; monitoring; nucleotide sequences;     Show all 7 Subjects
Abstract:
... An examination of the nucleic acid sequence alignment of 48 full-length rubella virus genomes revealed that the 5′ terminus of the genome is more conserved than the commonly used detection windows for rubella virus RNA located in the E1 protein coding region, suggesting that the 5′ terminus could be a target for improving detection of all rubella virus genotypes. Two candidate primer sets were tes ...
DOI:
10.1016/j.jviromet.2022.114555

8. Research progress of reduced amino acid alphabets in protein analysis and prediction

Author:
Yuchao Liang; Siqi Yang; Lei Zheng; Hao Wang; Jian Zhou; Shenghui Huang; Lei Yang; Yongchun Zuo
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 3503-3510
ISSN:
2001-0370
Subject:
sequence alignment,   etc   ; amino acid composition; amino acid sequences; amino acids; biotechnology; prediction;     Show all 6 Subjects
Abstract:
... Proteins are the executors of cellular physiological activities, and accurate structural and function elucidation are crucial for the refined mapping of proteins. As a feature engineering method, the reduction of amino acid composition is not only an important method for protein structure and function analysis, but also opens a broad horizon for the complex field of machine learning. Representing ...
DOI:
10.1016/j.csbj.2022.07.001

9. Crystal structure of the BAZ2B TAM domain

Author:
Yingying Feng; Sizhuo Chen; Mengqi Zhou; Jin Zhang; Jinrong Min; Ke Liu
Source:
Heliyon 2022 v.8 no.7 pp. e09873
ISSN:
2405-8440
Subject:
sequence alignment,   etc   ; DNA; crystal structure; epigenetics; haploinsufficiency; loss-of-function mutation; methylation; nucleosomes;     Show all 8 Subjects
Abstract:
... BAZ2B is a regulatory subunit of the ISWI (Imitation Switch) remodeling complex and engages in nucleosome remodeling. Loss-of-function and haploinsufficiency of BAZ2B are associated with different diseases. BAZ2B is a large multidomain protein. In addition to the epigenetic reader domains plant homeodomain (PHD) and bromodomain (BRD), BAZ2B also has a Tip5/ARBP/MBD (TAM) domain. Sequence alignment ...
DOI:
10.1016/j.heliyon.2022.e09873

10. Fine mapping and candidate gene analysis of qGL10 affecting rice grain length

Author:
Tengkui Chen; Lixin Luo; Zhe Zhao; Hui Wang; Chun Chen; Yongzhu Liu; Xinchang Li; Tao Guo; Wuming Xiao
Source:
crop journal 2022 pp. -
ISSN:
2214-5141
Subject:
sequence alignment,   etc   ; Oryza sativa; backcrossing; cultivars; genes; haplotypes; loci; promoter regions; rice; selfing;     Show all 10 Subjects
Abstract:
... Grain size influences the yield and quality of rice (Oryza sativa L.), and grain length is one of the component traits of grain size. In this study, a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428, with short grain size, as the recipient parent and indica rice cultivar ZYX, with long grain size, as the donor parent, by multi-generation backcrossing ...
DOI:
10.1016/j.cj.2022.06.013

11. Novel characteristics of Chinese NADC34‐like PRRSV during 2020–2021

Author:
Hu Xu; Chao Li; Wansheng Li; Jing Zhao; Bangjun Gong; Qi Sun; Yan‐Dong Tang; Lirun Xiang; Chaoliang Leng; Jinmei Peng; Qian Wang; Fandan Meng; Ying Yu; Tongqing An; Xuehui Cai; Zhi‐Jun Tian; Hongliang Zhang
Source:
Transboundary and emerging diseases 2022 v.69 no.5 pp. e3215
ISSN:
1865-1674
Subject:
sequence alignment,   etc   ; amino acids; genome; phylogeny; porcine reproductive and respiratory syndrome; viruses; China;     Show all 7 Subjects
Abstract:
... NADC34‐like porcine reproductive and respiratory syndrome virus (PRRSV) strains were first detected in China in 2017, with epidemic potential. In this study, the phylogenetic, epidemic, and recombinant properties of NADC34‐like PRRSV in China were evaluated comprehensively. From 2020 to October 2021, 82 NADC34‐like PRRSV isolates were obtained from 433 PRRSV‐positive clinical samples. These strain ...
DOI:
10.1111/tbed.14485

12. Extracting Land Use Change Patterns of Rural Town Settlements with Sequence Alignment Method

Author:
Senkai Xie; Wenjia Zhang; Yi Zhao; De Tong
Source:
Land 2022 v.11 no.2 pp. -
ISSN:
2073-445X
Subject:
sequence alignment,   etc   ; issues and policy; land; land use change; river deltas; rivers; urbanization; China;     Show all 8 Subjects
Abstract:
... Understanding land use change patterns of rural town settlements (RTSs) is crucial for rural and small-town planning; however, few studies have explored pattern mining approaches to RTS trajectory analysis. In this study, we adopted a novel method by building sequence alignment method (SAM) to detect representative trajectory clusters of land use change of 1158 RTSs in seven waves from 1980 to 201 ...
DOI:
10.3390/land11020313

13. Structure‐based prediction of the IgE epitopes of the major dog allergen Can f 1

Author:
Masatoshi Nakatsuji; Keisuke Sugiura; Keisuke Suda; Michiko Sakurai; Miki Ubatani; Haruka Muroya; Rina Okubo; Ryo Noguchi; Yoichi Kamata; Yuma Fukutomi; Osamu Ishibashi; Shigenori Nishimura; Takashi Inui
Source:
FEBS journal 2022 v.289 no.6 pp. 1668-1679
ISSN:
1742-464X
Subject:
sequence alignment,   etc   ; X-ray diffraction; alanine; allergens; crystal structure; dogs; epitopes; hypersensitivity; mutation; prediction;     Show all 10 Subjects
Abstract:
... Allergy to dogs has become increasingly prominent worldwide. Seven dog allergens have been identified, including Canis familiaris allergen 1–7 (Can f 1–7). Although Can f 1 is a major dog allergen sensitized to 50–75% of dog‐allergic subjects, its IgE epitopes have not been identified. The structural analysis of an allergen is important to identify conformational epitopes. In this study, we genera ...
DOI:
10.1111/febs.16252

14. Establishment of a dna barcoding database for legume and grass species identification

Author:
Yongqing Li; Zunongjiang A. La Bu; Lijun Cao; Shengguo Zhao
Source:
Legume research 2022 v.45 no.6 pp. 659-668
ISSN:
0976-0571
Subject:
sequence alignment,   etc   ; DNA; DNA barcoding; databases; forage; grasses; haplotypes; legumes; mutation; research; species identification;     Show all 11 Subjects
Abstract:
... DNA barcoding, an emerging approach, is being widely used to accurately and quickly identify species using conserved DNA sequences. Herein we designed seven universal primers for matK (matKI, matK2, matK3 and matK4), rbcL, psbA-trnH and ITS based on their nucleotide sequences in GenBank to amplify 40 species of leguminosae and grass forages. Sequence alignment was performed using MEGA 5.0 and hapl ...
DOI:
10.18805/AF-727

15. Genome‐wide characterization of caspase genes in Japanese pufferfish, Takifugu rubripes, and expression profiles in response to Vibrio harveyi infection

Author:
Xu Yang; Xia Liu; Zhen Yang; Yude Guan; Ruihu Zhao; Hongyu Peng; Xinyu Cao; Minghong Gao; Shuhui Wang; Chen Jiang
Source:
Journal of the World Aquaculture Society 2022 v.53 no.4 pp. 910-923
ISSN:
0893-8849
Subject:
sequence alignment,   etc   ; Takifugu rubripes; Vibrio harveyi; apoptosis; aquaculture; bioinformatics; caspases; inflammation; intestines; liver; phylogeny;     Show all 11 Subjects
Abstract:
... Caspases, also known as cysteine‐dependent aspartate‐directed proteases, play an important role in regulating apoptosis during development and inflammation. In this study, 10 caspase genes were characterized by searching the Japanese pufferfish genome using various bioinformatics methods, such as multiple sequence alignment and phylogenetic analysis. Additionally, we characterized the caspase gene ...
DOI:
10.1111/jwas.12904

16. Molecular cloning and functional characterization of KCNQ1 in shell biomineralisation of pearl oyster Pinctada fucata martensii

Author:
Panpan Xiong; Gaoyou Yao; Hua Zhang; Maoxian He
Source:
Gene 2022 v.821 pp. 146285
ISSN:
0378-1119
Subject:
sequence alignment,   etc   ; Pinctada fucata; biomineralization; genes; heart; osteoblasts; oysters; polypeptides; potassium channels; shellfish; ultrastructure;     Show all 11 Subjects
Abstract:
... KCNQ1, a voltage-gated potassium ion channel, plays an important role in various physiological processes, including osteoblast differentiation in higher animals. However, its function in lower invertebrates such as marine shellfish remains poorly understood. Pearl oysters, such as P. fucata martensii, are ideal for studying biomineralisation. In this study, a full-length cDNA of KCNQ1 from P. fuca ...
DOI:
10.1016/j.gene.2022.146285

17. Biodiversity of N-acyl homoserine lactonase (aiiA) gene from Bacillus subtilis

Author:
Ahmed O. Noor; Diena M. Almasri; A.F. Basyony; Amgad Albohy; Latifah S. Almutairi; Sarah S. Alhammadi; Maryam A. Alkhamisi; Shahad A. Alsharif; Mahmoud A. Elfaky
Source:
Microbial pathogenesis 2022 v.166 pp. 105543
ISSN:
0882-4010
Subject:
sequence alignment,   etc   ; Bacillus subtilis; biodiversity; biofilm; genes; genetic databases; homoserine; lactones; ligands; mutation; pathogenesis; virulence;     Show all 12 Subjects
Abstract:
... Microorganisms rely on the benefit of using chemical signals called autoinducers (AIs) as a connection matter in term of population, this mechanism is known as quorum sensing (QS). Quorum sensing is responsible for formation of biofilm together with virulence in bacteria. The most known QS molecule is N-acyl homoserine lactones (AHLs). A lot of degrading enzymes including lactonases that open the ...
DOI:
10.1016/j.micpath.2022.105543

18. SaAlign: Multiple DNA/RNA sequence alignment and phylogenetic tree construction tool for ultra-large datasets and ultra-long sequences based on suffix array

Author:
Ziyuan Wang; Junjie Tan; Yanling Long; Yijia Liu; Wenyan Lei; Jing Cai; Yi Yang; Zhibin Liu
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 1487-1493
ISSN:
2001-0370
Subject:
sequence alignment,   etc   ; DNA; algorithms; bioinformatics; biotechnology; computer software; data collection; mitochondrial genome; nucleotide sequences; phylogeny;     Show all 10 Subjects
Abstract:
... Multiple DNA/RNA sequence alignment is an important fundamental tool in bioinformatics, especially for phylogenetic tree construction. With DNA-sequencing improvements, the amount of bioinformatics data is constantly increasing, and various tools need to be iterated constantly. Mitochondrial genome analyses of multiple individuals and species require bioinformatics software; therefore, their perfo ...
DOI:
10.1016/j.csbj.2022.03.018

19. Diversity of phosphagen kinases in annelids: The first sequence report for a putative opheline kinase

Author:
Daichi Yano; Kouji Uda; Masakazu Nara; Tomohiko Suzuki
Source:
Comparative biochemistry and physiology 2022 v.257 pp. 110662
ISSN:
1096-4959
Subject:
sequence alignment,   etc   ; Escherichia coli; Polychaeta; RNA; amino acid sequences; amino acids; creatine kinase; mitochondria; phylogeny; physiology;     Show all 10 Subjects
Abstract:
... Opheline kinase (OK) is one of the phosphagen kinases (PKs) restricted to annelids, but the amino acid sequence has not been determined yet. The OK enzyme was isolated in 1966 from the polychaete Ophelia neglecta (Opheliidae) and shown to have somewhat broader activities for the various substrates opheline, lombricine and taurocyamine. To determine the OK sequence, we analyzed the RNA sequencing d ...
DOI:
10.1016/j.cbpb.2021.110662

20. Genome-wide characterization of Histone gene family and expression profiling during microspore development in radish (Raphanus sativus L.)

Author:
Qijiao Wang; Lianxue Fan; Xiaojun Su; Jiali Ying; Liang Xu; Cui Li; Yan Wang; Liwang Liu
Source:
Gene 2022 v.815 pp. 146180
ISSN:
0378-1119
Subject:
sequence alignment,   etc   ; DNA; Raphanus sativus; chromatin; doubled haploids; exons; histones; introns; phylogeny; radishes; transcription (genetics); transcriptomics;     Show all 12 Subjects
Abstract:
... Histone, a predominant protein component of chromatin, participates in DNA packaging and transcriptional regulation. However, the available information of Histone gene family is limited in radish. In this study, a total of 42 Histone gene family members were identified from the radish genome. Sequence alignment and phylogenetic analyses classified the Histone family into three groups (H2A, H2B and ...
DOI:
10.1016/j.gene.2021.146180