Gene Sequences of Potential Targets of Insecticidal PF2 Lectin Identified from the Larval De Novo Transcriptome of the Mexican Bean Weevil (Zabrotes Subfasciatus; Boheman 1833)

The available genomic and proteomic information of non-model organisms is often underrepresented in public databases hindering their study at molecular, cellular, and physiological levels. Information on Zabrotes subfasciatus (Mexican bean weevil) is poorly represented in databases, yet it is a major pest of common beans. We report the transcriptome of Z. subfasciatus larvae; transcripts were sequenced using an Illumina RNA-Seq technology and assembled de novo identifying 29,029 unigenes with an average size of 1168 bp and an N50 value of 2196 bp. About 15,124 unigenes (52%) were functionally annotated and categorized. Further analysis revealed 30 unigene sequences encoding putative targets of the insecticidal PF2 lectin. The complete deduced amino acid sequences of eight selected proteins potentially related to insecticidal mechanism of Palo Fierro 2 (PF2) were used for predicting probable N-glycosylation sites and analyzing phylogenetic relationships with insect sequences. This work provides a dramatic increase in the genetic resources available for Coleopterans and set the basis for developing future studies on biological aspects and potential control strategies for Z. subfasciatus.

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Uncovering thousands of new HLA antigens and phosphopeptides with deep learning-based sequence-mask-search de novo peptide sequencing framework

10.1101/667527 ◽

2019 ◽

Author(s):

Korrawe Karunratanakul ◽

Hsin-Yao Tang ◽

David W. Speicher ◽

Ekapol Chuangsuwanich ◽

Sira Sriswasdi

Keyword(s):

Deep Learning ◽

Amino Acid ◽

De Novo ◽

Hla Antigens ◽

Peptide Identification ◽

Peptide Sequencing ◽

Amino Acid Sequences ◽

Mass Spectrometry Data ◽

Model Organisms ◽

Invaluable Tool

ABSTRACTTypical analyses of mass spectrometry data only identify amino acid sequences that exist in reference databases. This restricts the possibility of discovering new peptides such as those that contain uncharacterized mutations or originate from unexpected processing of RNAs and proteins. De novo peptide sequencing approaches address this limitation but often suffer from low accuracy and require extensive validation by experts. Here, we develop SMSNet, a deep learning-based hybrid de novo peptide sequencing framework that achieves >95% amino acid accuracy while retaining good identification coverage. Applications of SMSNet on landmark proteomics and peptideomics studies reveal over 10,000 previously uncharacterized HLA antigens and phosphopeptides and in conjunction with database-search methods, expand the coverage of peptide identification by almost 30%. The power to accurately identify new peptides of SMSNet would make it an invaluable tool for any future proteomics and peptidomics studies – especially cancer neoantigen discovery and proteome characterization of non-model organisms.

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Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

Methods in Ecology and Evolution ◽

10.1111/2041-210x.13562 ◽

2021 ◽

Cited By ~ 1

Author(s):

José Cerca ◽

Marius F. Maurstad ◽

Nicolas C. Rochette ◽

Angel G. Rivera‐Colón ◽

Niraj Rayamajhi ◽

...

Keyword(s):

De Novo ◽

Model Organisms

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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽

10.3390/ani11082226 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2226

Author(s):

Sazia Kunvar ◽

Sylwia Czarnomska ◽

Cino Pertoldi ◽

Małgorzata Tokarska

Keyword(s):

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Model Organism ◽

Genotyping By Sequencing ◽

Model Organisms ◽

European Bison ◽

Model Animal ◽

Pcr Duplicates ◽

Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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The brain transcriptome of the wolf spider, Schizocosa ocreata

BMC Research Notes ◽

10.1186/s13104-021-05648-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Daniel Stribling ◽

Peter L. Chang ◽

Justin E. Dalton ◽

Christopher A. Conow ◽

Malcolm Rosenthal ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Wolf Spiders ◽

Schizocosa Ocreata ◽

Genomic Studies ◽

The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

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Molecular detection and genetic diversity of Leucocytozoon sabrazesi in chickens in Thailand

Scientific Reports ◽

10.1038/s41598-021-96241-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Runglawan Chawengkirttikul ◽

Witchuta Junsiri ◽

Amaya Watthanadirek ◽

Napassorn Poolsawat ◽

Sutthida Minsakorn ◽

...

Keyword(s):

Genetic Diversity ◽

Egg Production ◽

Control Strategies ◽

Amino Acid Sequences ◽

Economic Losses ◽

Nested Polymerase Chain Reaction ◽

Blood Samples ◽

Tropical Regions ◽

Vaccination Programs ◽

High Entropy

AbstractLeucocytozoon sabrazesi is the intracellular protozoa of leucocytozoonosis, which is transmitted by the insect vectors and affects chickens in most subtropical and tropical regions of the globe, except South America, and causing enormous economic losses due to decreasing meat yield and egg production. In this study, L. sabrazesi gametocytes have been observed in the blood smears, and molecular methods have been used to analyse the occurrence and genetic diversity of L. sabrazesi in blood samples from 313 chickens raised in northern, western and southern parts of Thailand. The nested polymerase chain reaction (nested PCR) assay based on the cytb gene revealed that 80.51% (252/313) chickens were positive of L. sabrazesi. The phylogenetic analysis indicated that L. sabrazesi cytb gene is conserved in Thailand, showed 2 clades and 2 subclades with similarity ranged from 89.5 to 100%. The diversity analysis showed 13 and 18 haplotypes of the sequences from Thailand and from other countries, respectively. The entropy analyses of nucleic acid sequences showed 26 high entropy peaks with values ranging from 0.24493 to 1.21056, while those of amino acid sequences exhibited 5 high entropy peaks with values ranging from 0.39267 to 0.97012. The results; therefore, indicate a high molecular occurrence of L. sabrazesi in chicken blood samples with the associated factors that is statistically significant (p < 0.05). Hence, our results could be used to improve the immunodiagnostic methods and to find appropriate preventive control strategies or vaccination programs against leucocytozoonosis in order to mitigate or eliminate the harmful impact of this infection on chicken industry.

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Eco-Environmental Aspects of COVID-19 Pandemic and Potential Control Strategies

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18073488 ◽

2021 ◽

Vol 18 (7) ◽

pp. 3488

Author(s):

Rashid Nazir ◽

Jawad Ali ◽

Ijaz Rasul ◽

Emilie Widemann ◽

Sarfraz Shafiq

Keyword(s):

Control Strategies ◽

Public Awareness ◽

Noise Pollution ◽

Environmental Aspects ◽

Potential Control ◽

Health Infrastructure ◽

The People ◽

Slum Dwellers ◽

Hospital Wastes ◽

Future Outbreak

A new coronavirus-strain from a zoonotic reservoir (probably bat)—termed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—has recently claimed more than two million deaths worldwide. Consequently, a burst of scientific reports on epidemiology, symptoms, and diagnosis came out. However, a comprehensive understanding of eco-environmental aspects that may contribute to coronavirus disease 2019 (COVID-19) spread is still missing, and we therefore aim to focus here on these aspects. In addition to human–human direct SARS-CoV-2 transmission, eco-environmental sources, such as air aerosols, different public use objects, hospital wastes, livestock/pet animals, municipal wastes, ventilation facilities, soil and groundwater potentially contribute to SARS-CoV-2 transmission. Further, high temperature and humidity were found to limit the spread of COVID-19. Although the COVID-19 pandemic led to decrease air and noise pollution during the period of lockdown, increased use of masks and gloves is threatening the environment by water and soil pollutions. COVID-19 badly impacted all the socio-economic groups in different capacities, where women, slum dwellers, and the people lacking social protections are the most vulnerable. Finally, sustainable strategies, waste management, biodiversity reclaim, eco-friendly lifestyle, improved health infrastructure and public awareness, were proposed to minimize the COVID-19 impact on our society and environment. These strategies will seemingly be equally effective against any future outbreak.

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Cloning and sequence analysis of cDNAs encoding the α1, α2 and α3 chains of mouse collagen VI

Biochemical Journal ◽

10.1042/bj2910787 ◽

1993 ◽

Vol 291 (3) ◽

pp. 787-792 ◽

Cited By ~ 8

Author(s):

R Z Zhang ◽

T C Pan ◽

R Timpl ◽

M L Chu

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Untranslated Regions ◽

Cdna Libraries ◽

Cdna Clones ◽

Collagen Vi ◽

Central Segment ◽

Glycosylation Sites ◽

Key Features ◽

Triple Helical Domain

cDNA clones encoding the alpha 1, alpha 2 and alpha 3 chains of mouse collagen VI have been isolated by screening cDNA libraries with the corresponding human probes. The composite cDNAs for the alpha 1, alpha 2, and alpha 3 chains are 2.5, 1.6 and 2.9 kb in size respectively. The alpha 1 and alpha 2 cDNAs encode the C-terminal portions of the chains as well as the entire 3′-untranslated regions, while the alpha 3 cDNAs encode a central segment of 959 amino acids flanking the triple-helical domain. The deduced amino acid sequences share 86-88% identity with the human counterparts and 67-73% identity with the chicken equivalents. Alignment of the deduced amino acid sequences of mouse, human and chicken collagens reveal that the key features of the protein, including the cysteine residues, imperfections in the Gly-Xaa-Xaa regions, Arg-Gly-Asp sequences and potential N-glycosylation sites, are mostly conserved.

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Comparison of seed consumption and the practical use of insect weight in determining effects of host seed on the Mexican bean weevil, Zabrotes subfasciatus (Boh.)

Journal of Stored Products Research ◽

10.1016/0022-474x(92)90001-7 ◽

1992 ◽

Vol 28 (4) ◽

pp. 225-234 ◽

Cited By ~ 6

Author(s):

Peter F. Credland ◽

Julie Dendy

Keyword(s):

Bean Weevil ◽

Zabrotes Subfasciatus

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Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge

mSystems ◽

10.1128/msystems.00113-18 ◽

2018 ◽

Vol 3 (5) ◽

Cited By ~ 6

Author(s):

Sean Ting-Shyang Wei ◽

Yu-Wei Wu ◽

Tzong-Huei Lee ◽

Yi-Shiang Huang ◽

Cheng-Yu Yang ◽

...

Keyword(s):

16S Rrna ◽

De Novo ◽

Anthropogenic Impacts ◽

Sequence Similarity ◽

Community Level ◽

Model Organisms ◽

Substrate Uptake ◽

Functional Responses ◽

Content Type ◽

Rare Biosphere

ABSTRACTThe 2,3-secopathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacteriumSterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity toStl. denitrificansare cholesterol degraders and members of the rare biosphere. Metatranscriptomic and metabolite analyses show that these degraders adopt the 2,3-secopathway to sequentially catalyze the side chain and sterane of cholesterol and that two molybdoenzymes—steroid C25 dehydrogenase and 1-testosterone dehydrogenase/hydratase—are crucial for these bioprocesses, respectively. The metatranscriptome further suggests that these betaproteobacterial degraders display chemotaxis and motility toward cholesterol and that FadL-like transporters may be the key components for substrate uptake. Also, these betaproteobacteria are capable of transporting micronutrients and synthesizing cofactors essential for cellular metabolism and cholesterol degradation; however, the required cobalamin is possibly provided by cobalamin-de novo-synthesizing gamma-, delta-, and betaproteobacteria via the salvage pathway. Overall, our results indicate that the ability to degrade cholesterol in sludge communities is reserved for certain rare biosphere members and that C25 dehydrogenase can serve as a biomarker for sterol degradation in anoxic environments.IMPORTANCESteroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactorde novosynthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.

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