M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Abstract Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence–absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.

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M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Access Microbiology ◽

10.1099/acmi.ac2020.po1014 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Oren Avram ◽

Dana Rapoport ◽

Shir Portugez ◽

Tal Pupko

Keyword(s):

Large Scale ◽

Ad Hoc ◽

Evolutionary Dynamics ◽

Gene Annotation ◽

Gc Content ◽

Web Server ◽

Disease Outbreaks ◽

Open Reading Frames ◽

Microbial Genomics ◽

Bacterial Strains

Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment, and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface (Avram, et al., Nucleic Acids Res., 2019). Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/ [https://microbializer.tau.ac.il/].

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InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data

Nucleic Acids Research ◽

10.1093/nar/gkaa363 ◽

2020 ◽

Vol 48 (W1) ◽

pp. W200-W207

Author(s):

Simone Puccio ◽

Giorgio Grillo ◽

Arianna Consiglio ◽

Maria Felicia Soluri ◽

Daniele Sblattero ◽

...

Keyword(s):

Phage Display ◽

Large Scale ◽

High Throughput Sequencing ◽

Gene Annotation ◽

Web Server ◽

Next Generation Sequencing Data ◽

Sequencing Data ◽

Phage Display Technology ◽

Essential Information ◽

Research Fields

Abstract High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the ‘interactome sequencing’ approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains (‘domainome’) or epitopes (‘epitome’) from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/

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Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution

Planta ◽

10.1007/s00425-021-03717-x ◽

2021 ◽

Vol 254 (4) ◽

Author(s):

Giuseppe Andolfo ◽

Cristina S. Sánchez ◽

Joaquìn Cañizares ◽

Maria B. Pico ◽

Maria R. Ercolano

Keyword(s):

Large Scale ◽

Ad Hoc ◽

De Novo ◽

Gene Annotation ◽

Death Process ◽

Pcr Analysis ◽

Gene Gain ◽

R Genes ◽

Protein Classes ◽

Species Specific

Abstract Main conclusion Genome-wide annotation reveals that the gene birth–death process of the Cucurbita R family is associated with a species-specific diversification of TNL and CNL protein classes. Abstract The Cucurbitaceae family includes nearly 1000 plant species known universally as cucurbits. Cucurbita genus includes many economically important worldwide crops vulnerable to more than 200 pathogens. Therefore, the identification of pathogen-recognition genes is of utmost importance for this genus. The major class of plant-resistance (R) genes encodes nucleotide-binding site and leucine-rich repeat (NLR) proteins, and is divided into three sub-classes namely, TIR-NB-LRR (TNL), CC-NB-LRR (CNL) and RPW8-NB-LRR (RNL). Although the characterization of the NLR gene family has been carried out in important Cucurbita species, this information is still linked to the availability of sequenced genomes. In this study, we analyzed 40 de novo transcriptomes and 5 genome assemblies, which were explored to investigate the Cucurbita expressed-NLR (eNLR) and NLR repertoires using an ad hoc gene annotation approach. Over 1850 NLR-encoding genes were identified, finely characterized and compared to 96 well-characterized plant R-genes. The maximum likelihood analyses revealed an unusual diversification of CNL/TNL genes and a strong RNL conservation. Indeed, several gene gain and loss events have shaped the Cucurbita NLR family. Finally, to provide a first validation step Cucurbita, eNLRs were explored by real-time PCR analysis. The NLR repertories of the 12 Cucurbita species presented in this paper will be useful to discover novel R-genes.

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Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution

BMC Ecology and Evolution ◽

10.1186/s12862-021-01905-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

R. Huttener ◽

L. Thorrez ◽

T. In’t Veld ◽

M. Granvik ◽

L. Van Lommel ◽

...

Keyword(s):

Protein Evolution ◽

Large Scale ◽

Energy Homeostasis ◽

Gene Annotation ◽

Gc Content ◽

Regional Effects ◽

Genome Wide ◽

Protein Encoding ◽

Window Approach ◽

Avian Genomes

Abstract Background Approximately 1000 protein encoding genes common for vertebrates are still unannotated in avian genomes. Are these genes evolutionary lost or are they not yet found for technical reasons? Using genome landscapes as a tool to visualize large-scale regional effects of genome evolution, we reexamined this question. Results On basis of gene annotation in non-avian vertebrate genomes, we established a list of 15,135 common vertebrate genes. Of these, 1026 were not found in any of eight examined bird genomes. Visualizing regional genome effects by our sliding window approach showed that the majority of these "missing" genes can be clustered to 14 regions of the human reference genome. In these clusters, an additional 1517 genes (often gene fragments) were underrepresented in bird genomes. The clusters of “missing” genes coincided with regions of very high GC content, particularly in avian genomes, making them “hidden” because of incomplete sequencing. Moreover, proteins encoded by genes in these sequencing refractory regions showed signs of accelerated protein evolution. As a proof of principle for this idea we experimentally characterized the mRNA and protein products of four "hidden" bird genes that are crucial for energy homeostasis in skeletal muscle: ALDOA, ENO3, PYGM and SLC2A4. Conclusions A least part of the “missing” genes in bird genomes can be attributed to an artifact caused by the difficulty to sequence regions with extreme GC% (“hidden” genes). Biologically, these “hidden” genes are of interest as they encode proteins that evolve more rapidly than the genome wide average. Finally we show that four of these “hidden” genes encode key proteins for energy metabolism in flight muscle.

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Characterization and genome analysis of two novel Aeromonas hydrophila phages PZL-Ah1and PZL-Ah8

10.21203/rs.3.rs-933679/v1 ◽

2021 ◽

Author(s):

Huabo Yu ◽

Chao Feng ◽

Liang Zhang ◽

Teng Chi ◽

Yanling Qi ◽

...

Keyword(s):

Aeromonas Hydrophila ◽

Bacterial Infections ◽

Genomic Sequence ◽

Gene Annotation ◽

Gc Content ◽

Opportunistic Pathogen ◽

Open Reading Frames ◽

Genome Database ◽

Narrow Host Range ◽

Phage T7

Abstract Aeromonas hydrophila (A.hydrophila) is an opportunistic pathogen of fish-human-livestock, which poses a seriously affects to the development of aquaculture. Phage therapy is considered as a process to alternatively control bacterial infections and contaminations. In this study, the genomes of two Aeromonas hydrophila- specific phages PZL-Ah1 and PZL-Ah8 were isolated, characterized and genomic sequence analyzed. Transmission electron microscopy showed that the two phages had been classified as the member of the Podoviridae family. Both the two phages in this study had relatively narrow host range with lytic activity against Aeromonas spp. strains. However, they could lyse 3 common A.hydrophila strain. As revealed from the whole genomic sequence analysis, PZL-Ah1 and PZL-Ah8 coverd the double-stranded genome of 38,641 bp and 40,855 bp in length, with the GC content of 53.68% and 51.89%, respectively. Through gene comparison in NCBI database revealed that PZL-Ah1 and PZL-Ah8 were 97.67% − 95.51% identical to Stenotrophomonas phage IME15 and Aeromonas Phage T7-Ah. Phylogenetic analysis showed that PZL-Ah8, PZL-Ah1 and other two phages belonged to the same genus. A total of 44 and 52 open reading frames (ORFs) were predicted in the PZL-Ah1 and PZL-Ah8 genome, respectively. In the process of gene annotation, 28 (63.6%) ORFs in PZL-Ah1 and 29 (55.8%) ORFs in PZL-Ah8 were known to functional proteins in NCBI database, while the remaining ORFs were classified as “hypothetical proteins”, whose functions were yet unknown. By comparing, ORF 02, ORF 29 and ORF 04 in PZL-Ah1, ORF24 in PZL-Ah8 were responsible for the host cell lysis. In conclusion, genomic studies of these two novel phages would lay the foundation for expanding the phage genome database and providing good candidates for phage typing applications.

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Phyto-fabrication of Iron Nanoparticles: Characterization and Antibacterial Capacity

Current Nanoscience ◽

10.2174/1573413716999200817105934 ◽

2020 ◽

Vol 16 ◽

Author(s):

Asma S. Algebaly ◽

Afrah E. Mohammed ◽

Mudawi M. Elobeid

Keyword(s):

Electron Microscopy ◽

Plant Extracts ◽

Large Scale ◽

Iron Nanoparticles ◽

Ethanolic Extract ◽

Green Technology ◽

Resistant Bacteria ◽

Scale Production ◽

Bacterial Strains ◽

Plant Sources

Introduction: Fabrication of iron nanoparticles (FeNPs) has recently gained a great concern for their varied applications in remediation technologies of the environment. Objective: The current study aimed to fabricate iron nanoparticles by green technology approach using different plant sources, Azadirachta indica leaf and Calligonum comosum root following two extraction methods. Methods: Currently, a mixture of FeCl2 and FeCl3 was used to react with the plant extracts which are considered as reducing and stabilizing agents for the generation of FeNPs in one step. Different techniques were used for FeNPs identification. Results: Immediately after mixing of the two reaction components, the color changed to dark brown as an indication of safe conversion of Fe ions to FeNPs, that later confirmed by zeta sizer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). FeNPs fabricated by C. comosum showed smaller size when compared by those fabricated by A. indica. Using both plant sources, FeNPs fabricated by the aqueous extract had smaller size in relation to those fabricated by ethanolic extract. Furthermore, antibacterial ability against two bacterial strains was approved. Conclusion: The current results indicated that, at room temperature plant extracts fabricated Fe ion to Fe nanoparticles, suggesting its probable usage for large scale production as well as its suitability against bacteria. It could also be recommended for antibiotic resistant bacteria.

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Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057105284342 ◽

2006 ◽

Vol 11 (3) ◽

pp. 236-246 ◽

Cited By ~ 6

Author(s):

Laurence H. Lamarcq ◽

Bradley J. Scherer ◽

Michael L. Phelan ◽

Nikolai N. Kalnine ◽

Yen H. Nguyen ◽

...

Keyword(s):

High Throughput ◽

Large Scale ◽

Strong Support ◽

Gc Content ◽

Rapid Identification ◽

Hairpin Rna ◽

Rna Sequences ◽

Short Hairpin ◽

Short Hairpin Rnas ◽

Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

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The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽

10.1093/genetics/162.4.1805 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1805-1810 ◽

Cited By ~ 1

Author(s):

Martin J Lercher ◽

Nick G C Smith ◽

Adam Eyre-Walker ◽

Laurence D Hurst

Keyword(s):

Population Genetics ◽

Large Scale ◽

Gc Content ◽

Nucleotide Composition ◽

Compositional Variation ◽

Mutation Bias ◽

Single Nucleotide ◽

Frequency Distributions ◽

Noncoding Regions ◽

Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

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Allometric Equations for Estimating Biomass and Carbon Stocks in Afforested Open Woodlands with Black Spruce and Jack Pine, in the Eastern Canadian Boreal Forest

Forests ◽

10.3390/f12010059 ◽

2021 ◽

Vol 12 (1) ◽

pp. 59

Author(s):

Olivier Fradette ◽

Charles Marty ◽

Pascal Tremblay ◽

Daniel Lord ◽

Jean-François Boucher

Keyword(s):

Large Scale ◽

Ad Hoc ◽

Black Spruce ◽

Tree Height ◽

Jack Pine ◽

Carbon Stocks ◽

Allometric Equations ◽

C Stocks ◽

The Difference ◽

Canadian Boreal Forest

Allometric equations use easily measurable biometric variables to determine the aboveground and belowground biomasses of trees. Equations produced for estimating the biomass within Canadian forests at a large scale have not yet been validated for eastern Canadian boreal open woodlands (OWs), where trees experience particular environmental conditions. In this study, we harvested 167 trees from seven boreal OWs in Quebec, Canada for biomass and allometric measurements. These data show that Canadian national equations accurately predict the whole aboveground biomass for both black spruce and jack pine trees, but underestimated branches biomass, possibly owing to a particular tree morphology in OWs relative to closed-canopy stands. We therefore developed ad hoc allometric equations based on three power models including diameter at breast height (DBH) alone or in combination with tree height (H) as allometric variables. Our results show that although the inclusion of H in the model yields better fits for most tree compartments in both species, the difference is minor and does not markedly affect biomass C stocks at the stand level. Using these newly developed equations, we found that carbon stocks in afforested OWs varied markedly among sites owing to differences in tree growth and species. Nine years after afforestation, jack pine plantations had accumulated about five times more carbon than black spruce plantations (0.14 vs. 0.80 t C·ha−1), highlighting the much larger potential of jack pine for OW afforestation projects in this environment.

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Sensor System: A Survey of Sensor Type, Ad Hoc Network Topology and Energy Harvesting Techniques

Electronics ◽

10.3390/electronics10020219 ◽

2021 ◽

Vol 10 (2) ◽

pp. 219

Author(s):

Phuoc Duc Nguyen ◽

Lok-won Kim

Keyword(s):

Energy Harvesting ◽

Large Scale ◽

Ad Hoc ◽

Sensor Nodes ◽

Sensor System ◽

Wireless Sensor ◽

The Internet ◽

Original Research ◽

Energy Scavenging ◽

Term Operation

People nowadays are entering an era of rapid evolution due to the generation of massive amounts of data. Such information is produced with an enormous contribution from the use of billions of sensing devices equipped with in situ signal processing and communication capabilities which form wireless sensor networks (WSNs). As the number of small devices connected to the Internet is higher than 50 billion, the Internet of Things (IoT) devices focus on sensing accuracy, communication efficiency, and low power consumption because IoT device deployment is mainly for correct information acquisition, remote node accessing, and longer-term operation with lower battery changing requirements. Thus, recently, there have been rich activities for original research in these domains. Various sensors used by processing devices can be heterogeneous or homogeneous. Since the devices are primarily expected to operate independently in an autonomous manner, the abilities of connection, communication, and ambient energy scavenging play significant roles, especially in a large-scale deployment. This paper classifies wireless sensor nodes into two major categories based the types of the sensor array (heterogeneous/homogeneous). It also emphasizes on the utilization of ad hoc networking and energy harvesting mechanisms as a fundamental cornerstone to building a self-governing, sustainable, and perpetually-operated sensor system. We review systems representative of each category and depict trends in system development.

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