1.

- Title: Bioinformatic Analysis of ABCA1 Gene Expression in Smoking and Chronic Obstructive
Pulmonary Disease
Author(s): Kotlyarov, S (Kotlyarov, Stanislav); Kotlyarova, A (Kotlyarova, Anna)
Source: MEMBRANES Volume: 11 Issue: 9 Article Number: 674 DOI:
10.3390/membranes11090674 Published: SEP 2021
Abstract: Smoking is a key modifiable risk factor for developing the chronic obstructive pulmonary
disease (COPD). When smoking, many processes, including the reverse transport of cholesterol
mediated by the ATP binding cassette transporter A1 (ABCA1) protein are disrupted in the lungs.
Changes in the cholesterol content in the lipid rafts of plasma membranes can modulate the
function of transmembrane proteins localized in them. It is believed that this mechanism
participates in increasing the inflammation in COPD. Methods: Bioinformatic analysis of datasets
from Gene Expression Omnibus (GEO) was carried out. Gene expression data from datasets of
alveolar macrophages and the epithelium of the respiratory tract in smokers and COPD patients
compared with non-smokers were used for the analysis. To evaluate differentially expressed genes,
bioinformatic analysis was performed in comparison groups using the limma package in R (v. 4.0.2),
and the GEO2R and Phantasus tools (v. 1.11.0). Results: The conducted bioinformatic analysis
showed changes in the expression of the ABCA1 gene associated with smoking. In the alveolar
macrophages of smokers, the expression levels of ABCA1 were lower than in non-smokers. At the
same time, in most of the airway epithelial datasets, gene expression did not show any difference
between the groups of smokers and non-smokers. In addition, it was shown that the expression of
ABCA1 in the epithelial cells of the trachea and large bronchi is higher than in small bronchi.
Conclusions: The conducted bioinformatic analysis showed that smoking can influence the
expression of the ABCA1 gene, thereby modulating lipid transport processes in macrophages, which
are part of the mechanisms of inflammation development.

2.- Title: Using multiple-steps bioinformatic analysis to predict the potential microRNA targets by
cardiogenic HoxA11
Author(s): Wang, CY (Wang, Chien-Ying); Liu, SY (Liu, Szu-Yuan); Kuo, FH (Kuo, Fu-Hsuan); Lin, HF
(Lin, Heng-Fu); Liu, CY (Liu, Chao-Yu); Yang, YP (Yang, Yi-Ping); Tsai, FT (Tsai, Fu-Ting); Huang, WC
(Huang, Wei-Chun); Tarng, YW (Tarng, Yih-Wen); Lin, HC (Lin, Hsin-Chi); Lu, KH (Lu, Kai-Hsi); Yu, WC
(Yu, Wen-Chung); Yang, MY (Yang, Meng-Yin)
Source: JOURNAL OF THE CHINESE MEDICAL ASSOCIATION Volume: 84 Issue: 1 Pages: 68-72 DOI:
10.1097/JCMA.0000000000000397 Published: JAN 2021
Abstract: Background: In this study, our major aim is to using multiple-steps bioinformatic analysis
to predict cardiogenic genes with targeting mRNA profiling for predicting cardiogenic HoxA11 gene.
Methods: We first analyzed the microarray data with bioinformatic measurement, including
combining with panel module 1 (mouse embryonic stem cells), panel module 2 (mouse induced
pluripotent stem cells), and panel module 3 (gene list form literature of heart development). A
literature-based comparison of the two microarrays and a software-based (Targetscan program, )
comparative analysis of the two datasets. Furthermore, we select the common central pathways
and potential candidate genes involved in the cardiomyocyte-lineaged differentiation and
development.
Results: Schematic presentation of a putative miR181a target site in Hox-A11 3 ' UTR. The
bioinformatic result showed that potential interacted cardiogenic targets of Tbx5, Tbx20, Mal2c,
Nkx2.5, cTNT, Cx43, MHC, and MCK in different treatment groups of pluripotent stem cells by using
a literature-based comparison of the two microarrays and a software-based gene-lineage system.
Conclusion: Our findings support that mir181a is an up-stream regulating microRNA to target the 3
' UTR of HoxA11 mRNA during the process of cardiomyocyte differentiation.
3.- Title: A bioinformatic analysis of microRNAs role in osteoarthritis
Author(s): Cong, L (Cong, L.); Zhu, Y (Zhu, Y.); Tu, G (Tu, G.)
Source: OSTEOARTHRITIS AND CARTILAGE Volume: 25 Issue: 8 Pages: 1362-1371 DOI:
10.1016/j.joca.2017.03.012 Published: AUG 2017
Abstract: Objective: To evaluate the underlying function of microRNAs (miRNAs) in osteoarthritis
(OA).
Design: A bioinformatic analysis of miRNAs-OA studies was completed in multiple databases. All
identified articles were assessed using specific inclusion and exclusion criteria (Eligible caseecontrol
studies for the present study included those which investigated miRNAs differential expression in
cartilage tissues and cells of OA and controls. Abstracts, case reports, conference presentations,
editorials, and expert opinions were excluded.). We performed bioinformatic analysis and assessed
which miRNAs are commonly elevated or decreased in cartilage of OA, and assessed putative targets
of these miRNAs using TargetScan, Database for Annotation, Visualization and Integrated Discovery
(DAVID), FunRich and String.
Results: Fifty seven studies were included in this study. Our current review has identified 46
differentially expressed miRNAs involved in autophagy, inflammation, chondrocyte apoptosis,
chondrocyte differentiation & homeostasis, chondrocyte metabolism and degradation of the
extracellular matrix (ECM). Additionally, our literature search identified a wide range of miRNAs that
have been shown to be differentially expressed in OA. The function of up-regulated miRNAs
primarily target nucleus, whereas the function of down-regulated miRNAs primarily target
transcription.
Conclusions: Comprehensive analysis of all miRNAs studies reveals cooperation in miRNA signatures
and suggests that there may be two biologically synergic classes of miRNAs that are associated with
OA. This finding suggests that miRNAs may be useful as diagnostic biomarkers and/or may provide
new therapeutic targets in OA. Furthermore, a better understanding of the targets of these miRNAs
will accelerate biomedical discoveries and improve clinical care based on new knowledge of OA-
related disease mechanisms.

4.- Title: Identification of Potential Hub Genes of Atherosclerosis Through Bioinformatic Analysis
Author(s): Yin, Y (Yin, Yang); Zou, YF (Zou, Yang-Fan); Xiao, Y (Xiao, Yu); Wang, TX (Wang, Tian-Xi);
Wang, YN (Wang, Ya-Ni); Dong, ZC (Dong, Zhi-Cheng); Huo, YH (Huo, Yu-Hu); Yao, BC (Yao, Bo-Chen);
Meng, LB (Meng, Ling-Bing); Du, SX (Du, Shuang-Xia)
Source: JOURNAL OF COMPUTATIONAL BIOLOGY Volume: 28 Issue: 1 Pages: 60-78 DOI:
10.1089/cmb.2019.0334 Early Access Date: APR 2020 Published: JAN 1 2021
Abstract: Cardiovascular and cerebrovascular diseases, which mainly consist of atherosclerosis (AS),
are major causes of death. A great deal of research has been carried out to clarify the molecular
mechanisms of AS. However, the etiology of AS remains poorly understood. To screen the potential
genes of AS occurrence and development, GSE43292 and GSE57691 were obtained from the Gene
Expression Omnibus (GEO) database in this study for bioinformatic analysis. First, GEO2R was used
to identify differentially expressed genes (DEGs) and the functional annotation of DEGs was
performed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.
The Search Tool for the Retrieval of Interacting Genes (STRING) tool was used to construct the
protein-protein interaction network and the most important modules and core genes were mined.
The results show that a total of 211 DEGs are identified. The functional changes of DEGs are mainly
associated with the cellular process, catalytic activity, and protein binding. Eighteen genes were
identified as core genes. Bioinformatic analysis showed that the core genes are mainly enriched in
numerous processes related to actin. In conclusion, the DEGs and hub genes identified in this study
may help us understand the potential etiology of the occurrence and development of AS.
5.- Title: Bioinformatic analysis of the S protein of human respiratory coronavirus
Author(s): Niu, Z (Niu, Zheng); Xu, SS (Xu, ShaSha); Zhang, JY (Zhang, JingYi); Zou, ZL (Zou, ZhuoLan);
Ren, LX (Ren, LiXin); Liu, XY (Liu, XiangYang); Zhang, SJ (Zhang, ShuJuan); Zou, H (Zou, Hong); Hu, X
(Hu, Xia); Wang, J (Wang, Jing); Zhang, L (Zhang, Li); Zhou, Y (Zhou, Yang); Song, ZH (Song, ZhenHui)
Source: MOLECULAR PHYLOGENETICS AND EVOLUTION Volume: 181 Article Number: 107704 DOI:
10.1016/j.ympev.2023.107704 Early Access Date: FEB 2023 Published: APR 2023
Abstract: The present study aimed to apply bioinformatic methods to analyze the structure of the S
protein of human respiratory coronaviruses, including severe respiratory disease syndrome
coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), human
coronavirus HKU1 (HCoV-HKU1), and severe respiratory disease syndrome coronavirus type 2 (SARS-
CoV-2). We predicted and analyzed the physicochemical properties, hydrophilicity and
hydrophobicity, transmembrane regions, signal peptides, phosphorylation and glycosylation sites,
epitopes, functional domains, and motifs of the S proteins of human respiratory coronaviruses. All
four S proteins contain a transmembrane region, which enables them to bind to host cell surface
receptors. All four S proteins contain a signal peptide, phosphorylation sites, glycosylation sites, and
epitopes. The predicted phos-phorylation sites might mediate S protein activation, the glycosylation
sites might affect the cellular orientation of the virus, and the predicted epitopes might have
implications for the design of antiviral inhibitors. The S proteins of all four viruses have two
structural domains, S1 (C-terminal and N-terminal domains) and S2 (ho-mology region 1 and 2). Our
bioinformatic analysis of the structural and functional domains of human respi-ratory coronavirus S
proteins provides a basis for future research to develop broad-spectrum antiviral drugs, vaccines,
and antibodies.

6.- Title: Bioinformatic analysis and functional predictions of selected regeneration-associated

transcripts expressed by zebrafish microglia
Author(s): Salia, OI (Salia, Ousseini Issaka); Mitchell, DM (Mitchell, Diana M.)
Source: BMC GENOMICS Volume: 21 Issue: 1 Article Number: 870 DOI: 10.1186/s12864-020-
07273-8 Published: DEC 7 2020
Abstract: BackgroundUnlike mammals, zebrafish have a remarkable capacity to regenerate a variety
of tissues, including central nervous system tissue. The function of macrophages in tissue
regeneration is of great interest, as macrophages respond and participate in the landscape of events
that occur following tissue injury in all vertebrate species examined. Understanding macrophage
populations in regenerating tissue (such as in zebrafish) may inform strategies that aim to
regenerate tissue in humans. We recently published an RNA-seq experiment that identified genes
enriched in microglia/macrophages in regenerating zebrafish retinas. Interestingly, a small number
of transcripts differentially expressed by retinal microglia/macrophages during retinal regeneration
did not have predicted orthologs in human or mouse. We reasoned that at least some of these genes
could be functionally important for tissue regeneration, but most of these genes have not been
studied experimentally and their functions are largely unknown. To reveal their possible functions,
we performed a variety of bioinformatic analyses aimed at identifying the presence of functional
protein domains as well as orthologous relationships to other species.ResultsOur analyses identified
putative functional domains in predicted proteins for a number of selected genes. For example, we
confidently predict kinase function for one gene, cytokine/chemokine function for another, and
carbohydrate enzymatic function for a third. Predicted orthologs were identified for some, but not
all, genes in species with described regenerative capacity, and functional domains were consistent
with identified orthologs. Comparison to other published gene expression datasets suggest that at
least some of these genes could be important in regenerative responses in zebrafish and not
necessarily in response to microbial infection.ConclusionsThis work reveals previously undescribed
putative function of several genes implicated in regulating tissue regeneration. This will inform
future work to experimentally determine the function of these genes in vivo, and how these genes
may be involved in microglia/macrophage roles in tissue regeneration.

7.- Title: Bioinformatic Anallysis and Subcellular Localization of Solanum lycopersicum ARF2
Author(s): Feng, YY (Feng Yuan-Yuan); Hou, P (Hou Pei); Li, YN (Li Ying-Nan); Liu, YS (Liu Yong-Sheng)
Source: PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS Volume: 39 Issue: 1 Pages: 51-58 DOI:
10.3724/SP.J.1206.2011.00197 Published: JAN 2012
Abstract: Auxin response factors (ARFs) are important transcription factors involved in auxin signal
transduction pathway. In order to elucidate the function of tomato A RF2, we isolated the SlARF2
gene and analyzed its molecular features, in addition, we observed the subcellular localization of
ARF2 in transgenic tomato plants. Physicochemical properties and molecular features of ARF2 were
predicted by bioinformatic approaches including physical and chemical properties analysis,
hydrophobicity analysis, domain analysis, phylogenetic tree analysis and subcellular localization
analysis. Moreover, the full-length of SlARF2 gene was amplified by RT-PCR, and a binary vector
consisting of ARF2 fused with the yellow fluorescent protein (YFP) coding sequence was further
constructed. Using the method of Agrobacterium-mediated transformation, the recombinant vector
was transformed into wild-type tomato, and the transgenic tomato plants were confirmed by PCR.
The roots of transgenic tomato seedlings were observed under a fluorescence microscope.
Bioinformatic analysis showed that the SlARF2 is an unstable soluble protein, which is rich in Ser,
Gly, Pro and Leu residues, and it has typical structure and functional domain of ARF family. Tomato
ARF2 shares 70.08 %, 66.94 %, and 60.87 % similarity in amino acid sequences with grapes, cassava
and Arabidopsis, respectively. Analyses of restriction enzyme digestion and sequencing confirmed
the expression vector pBA-ARF2-YFP was successfully constructed. PCR results showed the fusion
protein was expressed in transgenic tomato plants. The subcellular localization of SlARF2 was found
mostly in the nucleus. SlARF2 has the key characteristics of transcription factor, which is localized in
the nucleus, and it might play a pivotal role in tomato fruit development and ripening. This might
provide references for studying the function of SlARF2 gene.

8.- Title: Hydroxysteroid dehydrogenases (HSDs) in bacteria - A bioinformatic perspective

Author(s): Kisiela, M (Kisiela, Michael); Skarka, A (Skarka, Adam); Ebert, B (Ebert, Bettina);
Maser, E (Maser, Edmund)
Source: JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR
BIOLOGY Volume: 129 Issue: 1-2 Special Issue: SI Pages: 31-
46 DOI: 10.1016/j.jsbmb.2011.08.002 Published: MAR 2012
Abstract: Steroidal compounds including cholesterol, bile acids and steroid hormones play a central
role in various physiological processes such as cell signaling, growth, reproduction, and energy
homeostasis. Hydroxysteroid dehydrogenases (HSDs), which belong to the superfamily of short-
chain dehydrogenases/reductases (SDR) or aldo-keto reductases (AKR), are important enzymes
involved in the steroid hormone metabolism. HSDs function as an enzymatic switch that controls
the access of receptor-active steroids to nuclear hormone receptors and thereby mediate a fine-
tuning of the steroid response. The aim of this study was the identification of classified functional
HSDs and the bioinformatic annotation of these proteins in all complete sequenced bacterial
genomes followed by a phylogenetic analysis. For the bioinformatic annotation we constructed
specific hidden Markov models in an iterative approach to provide a reliable identification for the
specific catalytic groups of HSDs. Here, we show a detailed phylogenetic analysis of 3 alpha-, 7
alpha-, 12 alpha-HSDs and two further functional related enzymes (3-ketosteroid-Delta(1)-
dehydrogenase, 3-ketosteroid-Delta(4)(5 alpha)-dehydrogenase) from the superfamily of SDRs. For
some bacteria that have been previously reported to posses a specific HSD activity, we could
annotate the corresponding HSD protein. The dominating phyla that were identified to express
HSDs were that of Actinobacteria, Proteobacteria, and Firmicutes. Moreover, some evolutionarily
more ancient microorganisms (e.g., Cyanobacteria and Euryachaeota) were found as well. A large
number of HSD-expressing bacteria constitute the normal human gastro-intestinal flora. Another
group of bacteria were originally isolated from natural habitats like seawater, soil, marine and
permafrost sediments. These bacteria include polycyclic aromatic hydrocarbons-degrading species
such as Pseudomonas, Burkholderia and Rhodococcus. In conclusion, HSDs are found in a wide
variety of microorganisms including bacteria and archaea, suggesting that steroid metabolism is an
evolutionarily conserved mechanism that might serve different functions such as nutrient supply
and signaling.

9.- Title: Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-

specific positions responsible for discrimination of amidase and lipase activities
Author(s): Suplatov, DA (Suplatov, D. A.); Besenmatter, W (Besenmatter, W.); Svedas, VK
(Svedas, V. K.); Svendsen, A (Svendsen, A.)
Source: PROTEIN ENGINEERING DESIGN & SELECTION Volume: 25 Issue: 11 Special
Issue: SI Pages: 689-697 DOI: 10.1093/protein/gzs068 Published: NOV 2012
Abstract: Superfamily of alpha-beta hydrolases is one of the largest groups of structurally
related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study
how lipase and amidase catalytic activities are implemented into the same structural
framework. Subfamily-specific positions-conserved within lipases and peptidases but
different between them-that were supposed to be responsible for functional
discrimination have been identified. Mutations at subfamily-specific positions were used
to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling
was implemented to evaluate influence of selected residues on binding and catalytic
conversion of amide substrate by corresponding library of mutants. In silico screening was
applied to select reactive enzyme-substrate complexes that satisfy knowledge-based
criteria of amidase catalytic activity. Selected CALB variants with substitutions at
subfamily-specific positions Gly39, Thr103, Trp104, and Leu278 were produced and
showed significant improvement of experimentally measured amidase activity. Based on
these results, we suggest that value of subfamily-specific positions should be further
explored in order to develop a systematic tool to study structure-function relationship in
enzymes and to use this information for rational enzyme engineering.

10.- Title: Bioinformatic characterization of the extracellular lipases from Kluyveromyces

marxianus
Author(s): Martinez-Corona, R (Martinez-Corona, Ricardo); Marrufo, GV (Vazquez
Marrufo, Gerardo); Penagos, CC (Cortes Penagos, Carlos); Madrigal-Perez, LA (Alberto
Madrigal-Perez, Luis); Gonzalez-Hernandez, JC (Carlos Gonzalez-Hernandez, Juan)
Source: YEAST Volume: 37 Issue: 1 Pages: 149-162 DOI: 10.1002/yea.3449 Early Access
Date: DEC 2019 Published: JAN 2020
Abstract: Lipases are hydrolytic enzymes that break the ester bonds of triglycerides,
generating free fatty acids and glycerol. Extracellular lipase activity has been reported for
the nonconventional yeast Kluyveromyces marxianus, grown in olive oil as a substrate, and
the presence of at least eight putative lipases has been detected in its genome. However,
to date, there is no experimental evidence on the physiological role of the putative lipases
nor their structural and catalytic properties. In this study, a bioinformatic analysis of the
genes of the putative lipases from K. marxianus L-2029 was performed, particularly
identifying and characterizing the extracellular expected enzymes, due to their
biotechnological relevance. The amino acid sequence of 10 putative lipases, obtained by
in silico translation, ranged between 389 and 773 amino acids. Two of the analysed
putative proteins showed a signal peptide, 25 and 33 amino acids long for KmYJR107Wp
and KmLIP3p, and a molecular weight of 44.53 and 58.23 kDa, respectively. The amino acid
alignment of KmLIP3p and KmYJR107Wp with the crystallized lipases from a patatin and
the YlLip2 lipase from Yarrowia lipolytica, respectively, revealed the presence of the
hydrolase characteristic motifs. From the 3D models of putative extracellular K. marxianus
L-2029 lipases, the conserved pentapeptide of each was determined, being GTSMG for
KmLIP3p and GHSLG for KmYJR107Wp; besides, the genes of these two enzymes (LIP3 and
YJR107W) are apparently regulated by oleate response elements. The phylogenetic
analysis of all K. marxianus lipases revealed evolutionary affinities with lipases from
abH15.03, abH23.01, and abH23.02 families.

11.- Title: RNA-seq analysis in forest tree species: bioinformatic problems and solutions
Author(s): de Heredia, UL (Lopez de Heredia, Unai); Vazquez-Poletti, JL (Luis Vazquez-Poletti, Jose)
Source: TREE GENETICS & GENOMES Volume: 12 Issue: 2 Article Number: 30 DOI: 10.1007/s11295-
016-0995-x Published: APR 2016
Abstract: Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has
allowed a growing number of gene expression studies focused on forest trees in the last 5 years.
Bioinformatic analyses derived from RNA-seq of forest trees are particularly challenging, because
the massive genome length (similar to 20.1 Gbp for loblolly pine) and the absence of annotated
reference genomes require specific bioinformatic pipelines to obtain sound biological results. In the
present manuscript, we review common bioinformatic challenges that researchers need to consider
when analyzing RNA-seq data from forest tree species at the light of the experience acquired from
recent studies. Furthermore, we list bioinformatic pipelines and data processing software available
to overcome RNA-seq limitations. Finally, we discuss the impact of novel computation solutions,
such as the cloud computing paradigm that allows RNA-seq analysis even for small research centers
with limited resources.

12.- Title: A review of bioinformatic methods for forensic DNA analyses

Author(s): Liu, YY (Liu, Yao-Yuan); Harbison, S (Harbison, SallyAnn)
Source: FORENSIC SCIENCE INTERNATIONAL-GENETICS Volume: 33 Pages: 117-128 DOI:
10.1016/j.fsigen.2017.12.005 Published: MAR 2018
Abstract: Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial
analyses are three classes of markers which will play an important role in the future of forensic DNA
typing. The arrival of massively parallel sequencing platforms in forensic science reveals new
information such as insights into the complexity and variability of the markers that were previously
unseen, along with amounts of data too immense for analyses by manual means. Along with the
sequencing chemistries employed, bioinformatic methods are required to process and interpret this
new and extensive data. As more is learnt about the use of these new technologies for forensic
applications, development and standardization of efficient, favourable tools for each stage of data
processing is being carried out, and faster, more accurate methods that improve on the original
approaches have been developed. As forensic laboratories search for the optimal pipeline of tools,
sequencer manufacturers have incorporated pipelines into sequencer software to make analyses
convenient. This review explores the current state of bioinformatic methods and tools used for the
analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms
currently most widely used.
13.- Title: Predicting nucleosome positioning in genomes: Physical and bioinformatic approaches
Author(s): Scipioni, A (Scipioni, Anita); De Santis, P (De Santis, Pasquale)
Source: BIOPHYSICAL CHEMISTRY Volume: 155 Issue: 2-3 Pages: 53-64 DOI:
10.1016/j.bpc.2011.03.006 Published: MAY 2011
Abstract: In eukaryotic genomes, nucleosomes are responsible for packaging DNA and controlling
gene expression. For this reason, an increasing interest is arising on computational methods capable
of predicting the nucleosome positioning along genomes. In this review we describe and compare
bioinformatic and physical approaches adopted to predict nucleosome occupancy along genomes.
Computational analyses attempt at decoding the experimental nucleosome maps of genomes in
terms of certain dinucleotide step periodicity observed along DNA. Such investigations show that
highly significant information about the occurrence of a nucleosome along DNA is intrinsic in certain
features of the sequence suggesting that DNA of eukaryotic genomes encodes nucleosome
organization. Besides the bioinformatic approaches, physical models were proposed based on the
sequence dependent conformational features of the DNA chain, which govern the free energy
needed to transform recurrent DNA tracts along the genome into the nucleosomal shape.

14.- Title: Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments
Author(s): Marsh, JW (Marsh, James W.); Hayward, RJ (Hayward, Regan J.); Shetty, AC (Shetty, Amol
C.); Mahurkar, A (Mahurkar, Anup); Humphrys, MS (Humphrys, Michael S.); Myers, GSA (Myers,
Garry S. A.)
Source: BRIEFINGS IN BIOINFORMATICS Volume: 19 Issue: 6 Pages: 1115-1129 DOI:
10.1093/bib/bbx043 Published: NOV 2018
Abstract: Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and
replication; in turn, host cells respond to the invading pathogen through cascading changes in gene
expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial
virulence factors or host response pathways is crucial for improved diagnostics and therapeutics.
Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and
bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and
resolution of RNA sequencing technology and is applicable to any bacteria that interact with
eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory
protocols have been presented that outline the collection, extraction and sequencing of total RNA
for dRNA-Seq experiments, but there is relatively little guidance available for the detailed
bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a
Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic
analyses with currently available software tools.

15.- Title: Costimulation and allergic responses: Immune and bioinformatic analyses
Author(s): Jain, VV (Jain, Vipul V.); Perkins, DL (Perkins, David L.); Finn, PW (Finn, Patricia W.)
Source: PHARMACOLOGY & THERAPEUTICS Volume: 117 Issue: 3 Pages: 385-392 DOI:
10.1016/j.pharmthera.2007.12.002 Published: MAR 2008
Abstract: Asthma is a complex polygenic disease, the prevalence of which has been on the rise for
last few decades. Defining the underpinnings of allergic immune responses and the factors
predisposing to asthma are fundamental investigative challenges. T cell costimulatory pathways
play critical roles in the pathogenesis of asthma. In this review, we analyze the current state of the
art of T cell costimulation in allergic airway inflammation. Also, we discuss both immune and
bioinformatic approaches as potential strategies for analyzing multiple costimulatory pathways
relevant to asthma. (C) 2008 Elsevier Inc. All rights reserved.
16.- Title: Thrombin-like effect of an important green pit viper toxin, albolabrin: a bioinformatic
study
Author(s): Wiwanitkit, V (Wiwanitkit, Viroj)
Source: ARCHIVES OF TOXICOLOGY Volume: 80 Issue: 12 Pages: 829-832 DOI: 10.1007/s00204-
006-0108-y Published: DEC 2006
Abstract: The green pit viper venom has a major effect on the hematological system. Clinical
features of venomous snakebites vary from asymptomatic to fatal bleeding. The venom is found to
have a thrombin-like effect in vitro. Here, the author performs a bioinformatic analysis on the green
pit viper venom focusing on its thrombin-like effect. Sequence comparison between green pit viper
venom, albolabrin and thrombin was performed. In addition, the author performed a search for
other human proteins closely relating to the thrombin and created a multiple sequence alignment
phylogenetic tree to present the family tree of the thrombin, albolabrin and those proteins recorded
in the genomic database. In conclusion, the comparative sequence analysis between green pit viper
venom and thrombin gives several identities. The reported relationship on the phylogenetic tree
can match with the reported in vivo function of green pit viper. Explanations on the effect of green
pit viper toxin on the hemostasis can be derived from this study. Furthermore, future researches
based on the reported identities can be expected.

17.- Title: Bioinformatic Analysis of Toll-Like Receptor Sequences and Structures

Author(s): Monie, TP (Monie, Tom P.); Gay, NJ (Gay, Nicholas J.); Gangloff, M (Gangloff, Monique)
Edited by: McCoy CE
Source: TOLL-LIKE RECEPTORS, 2 EDITION: Practice and Methods Book Series: Methods in Molecular
Biology Volume: 1390 Pages: 29-39 DOI: 10.1007/978-1-4939-3335-8_2 Published: 2016
Abstract: Continual advancements in computing power and sophistication, coupled with rapid
increases in protein sequence and structural information, have made bioinformatic tools an
invaluable resource for the molecular and structural biologist. With the degree of sequence
information continuing to expand at an almost exponential rate, it is essential that scientists today
have a basic understanding of how to utilise, manipulate and analyse this information for the benefit
of their own experiments. In the context of Toll-Interleukin I Receptor domain containing proteins,
we describe here a series of the more common and user-friendly bioinformatic tools available as
Internet-based resources. These will enable the identification and alignment of protein sequences;
the identification of functional motifs; the characterisation of protein secondary structure; the
identification of protein structural folds and distantly homologous proteins; and the validation of
the structural geometry of modelled protein structures.