A reduced computational load protein coding predictor using equivalent amino acid sequence of DNA string with period-3 based time and frequency domain analysis

Development of efficient gene prediction algorithms is one of the fundamental efforts in gene prediction study in the area of genomics. In genomic signal processing the basic step of the identification of protein coding regions in DNA sequences is based on the period-3 property exhibited by nucleotides in exons. Several approaches based on signal processing tools and numerical representations have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new indicator sequence based on amino acid sequence, called as aminoacid indicator sequence, derived from DNA string that uses the existing signal processing based time-domain and frequency domain methods to predict these regions within the billions long DNA sequence of eukaryotic cells which reduces the computational load by one-third. It is known that each triplet of bases, called as codon, instructs the cell machinery to synthesize an amino acid. The codon sequence therefore uniquely identifies an amino acid sequence which defines a protein. Thus the protein coding region is attributed by the codons in amino acid sequence. This property is used for detection of period-3 regions using amino acid sequence. Physico-chemical properties of amino acids are used for numerical representation. Various accuracy measures such as exonic peaks, discriminating factor, sensitivity, specificity, miss rate, wrong rate and approximate correlation are used to demonstrate the efficacy of the proposed predictor. The proposed method is validated on various organisms using the standard data-set HMR195, Burset and Guigo and KEGG. The simulation result shows that the proposed method is an effective approach for protein coding prediction.

Pathogenicity and amino acid sequences of hemagglutinin cleavage site and neuraminidase stalk of differently passaged H9N2-avian influenza virus in broilers

Low pathogenic Avian Influenza (AI) virus has the ability to evolve to high pathogenic viruses resulting in significant economic losses in the poultry sector. This study aims at assessing the impact of H9N2 viral passaging in broilers and its relatedness to pathogenicity and amino acid (a.a) sequences of the hemagglutinin (HA) cleavage site and neuraminidase (NA) stalk. The original H9N2 AI virus (P0) was used to challenge ten-21 days old broilers. Individual recovery of H9N2 virus from homogenates of trachea, lungs and airsacs was attempted in 9 days old chicken embryos, as a conclusion of the first passage (P1). Tracheal isolates of H9N2 were passaged for a second (P2) and a third (P3) time in broilers, followed by a similar embryonic recovery procedure. The a.a. sequence of a part of HA1 cleavage site and Neuraminidase stalk were compared among the differently passaged viruses;an assessement of the relatedness of the determined a.a. sequences to the pathogenicity in broilers, based on frequency of mortality, morbidity signs, gross and microscopic lesions at 3 days post challenge with the P1, P2, and P3-H9N2, is concluded. An increase in certain morbidity signs and specific lesions was observed in P2- and P3-H9N2 challenged broilers compared to birds challenged with P1-H9N2. A conserved R-S-S-R amino acid sequence at the HA1 cleavage site was observed in the differently passaged H9N2, associated with a variability in the NA stalk-a.a sequences. The passaging of the low pathogenic H9N2 virus in broilers leads to a trend of increase in pathogenicity, manifested in higher frequency of morbidity signs, and of specific gross and microscopic lesions of the examined organs. This passaging was associated with a conserved a.a. sequence of the hemaglutinin cleavage site and a variability in the sequence of the neuraminidase stalk. A detailed study of the potential of the detected variability in the neuraminidase stalk of H9N2 in induction of a higher pathogenicity in broilers will be the subject of future investigations.

The structural analysis of protein sequences based on the quasi-amino acids code

Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Cenome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system （∑, ＋, ＊） is introduced, where ∑ is the set of 64 codons. According to the characteristics of （∑, ＋, ＊）, a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al （2003 J. Anhui Agricultural University 30 439）, the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that （ZU, ＋,×） is a field. Furthermore, the operational results display that the eodon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al （2002 Acta Biophysiea Siniea 18（1） 87）. The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of ＇the 64 codon assignments of mRNA to amino acids is probably completely wrong＇ proposed by Yang （2006 Progress in Modern Biomedicine 6 3）.

Prediction of the Helix/Sheet Content of Proteins from Their Primary Sequences by Neural Network Method

The amino acid composition and the biased auto-correlation function are considered as features, BP neural network algorithm is used to synthesize these features. The prediction accuracy of this method is verified by using the independent non-homologous protein database. It is shown that the average absolute errors for resubstitution test are 0.070 and 0.068 with the standard deviations 0.049 and 0.047 for the prediction of the content of α-helix and β-sheet respectively. For cross-validation test, the average absolute errors are 0.075 and 0.070 with the standard deviations 0.050 and 0.049 for the prediction of the content of α-helix and β-sheet respectively. Compared with the other methods currently available, the BP neural network method combined with the amino acid composition and the biased auto-correlation function features can effectively improve the prediction accuracy.

Phylogenetic Relationships of 11 Bumblebee Species (Hymenoptera:Apidae) Based on Mitochondrial Cytochrome b Gene Sequences

Phylogenetic relationships of 11 bumblebee species,including 5 subgenera:Bombus (5 species),Thoracobombus (3 species),Mendacibombus (1 species),Fervidobombus (1 species) and Pyrobombus (1 species),were analyzed based on the 357?bp mitochondrial cytochrome b gene sequences.There are 65 singleton polymorphic sites and 71 parsimony informative polymorphic sites in this DNA segment,and 45 polymorphic sites within the total 119 translated amino acids segment.Both NJ tree and MP tree show that Mendacibombus (B.avinovielllus) is basal to others,followed by Fervidobombus (B.pensylvanicus);Pyrobombus (B.impatiens) and Bombus are sister subgenera;the subgenus of Bombus is monophyletic,in which B.ignitus diverged first.

Rice bicoid-related cDNA sequence and its expression during early embryogenesis

Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accession number: AJ2771380), was isolated by screening of rice unmature seed cDNA library. Sequence analysis indicates that Rb24 contains a putative amino acid sequence, which is homologous to unique 8 amino acids sequence within Drosophila bicoid homeodomain (50% identity, 75% similarity) and involves a lys-9 in putative helix 3. Northern blot analysis of rice RNA has shown that this sequence is expressed in a tissue-specific manner. The transcript was detected strongly in young panicles, but less in young leaves and roots. This results are further confirmed with paraffin section in situ hybridization. The signal is intensive in rice globular embryo and located at the apical tip of the embryo, then, along with the development of embryo, the signal is getting reduced and transfers into both sides of embryo. The existence of bicoid-related sequence in rice embryo and the similarity of polar distribution of bicoid and Rb24 mRNA in early embryo development may implicates a conserved maternal regulation mechanism of body axis presents in Drosophila and in rice.

Branched-chain amino acids to tyrosine ratio value as a potential prognostic factor for hepatocellular carcinoma

The prognosis of hepatocellular carcinoma(HCC) depends on tumor extension as well as hepatic function.Hepatic functional reserve is recognized as a factor affecting survival in the treatment of HCC;the ChildPugh classif ication system is the most extensively used method for assessing hepatic functional reserve in patients with chronic liver disease,using serum albumin level to achieve accurate assessment of the status of protein metabolism.However,insuff icient attention has been given to the status of amino acid(AA) metabolism in chronic liver disease and HCC.Fischer's ratio is the molar ratio of branched-chain AAs(BCAAs:leucine,valine,isoleucine) to aromatic AAs(phenylalanine,tyrosine) and is important for assessing liver metabolism,hepatic functional reserve and the severity of liver dysfunction.Although this ratio is diff icult to determine in clinical situations,BCAAs/tyrosine molar concentration ratio(BTR) has been proposed as a simpler substitute.BTR correlates with various liver function examinations,including markers of hepatic f ibrosis,hepatic blood flow and hepatocyte function,and can thus be considered as reflecting the degree of hepatic impairment.This manuscript examines the literature to clarify whether BTR can serve as a prognostic factor for treatment of HCC.

Evolution from Primitive Life to Homo sapiens Based on Visible Genome Structures: The Amino Acid World

It is not too much to say that molecular biology, including genome research, has progressed based on the determination of nucleotide or amino acid sequences. However, these ap-proaches are limited to the analysis of relatively small numbers of the same genes among spe-cies. On the other hand, by graphical presenta-tion of the ratios of the numbers of amino acids present to the total numbers of amino acids presumed from the target gene(s) or genome or those of the numbers of nucleotides present to the total numbers of nucleotides calculated from the target gene(s) or genome, we can readily draw conclusions from extraordinarily huge data sets integrated by human intelli-gence. 1) Assuming polymerization of amino acids or nucleotides in a simulation analysis based on a random choice, proteins were formed by simple amino acid polymerization, while nucleotide polymerization to form nucleic acids encoding specific proteins needed certain specific control. These results proposed that protein formation chronologically preceded codon formation during the establishment of primitive life forms. In the prebiotic phase, amino acid composition was a dominant factor that determined protein characteristics;the “Amino Acid World”. 2) The genome is constructed homogeneou- sly from putative small units displaying similar codon usages and coding for similar amino acid compositions;the unit is a gene assembly en-coding 3,000 - 7,000 amino acid residues and this unit size is independent not only of genome size, but also of species. 3) In codon evolution, all nucleotide alterna-tions are correlated, not only in coding regions, but also in non-coding regions;the correlations can be expressed by linear formulas;y = ax + b, where “y” and “x” represent nucleotide con-tents, and “a” and “b” are constant. 4) The basic pattern of cellular amino acid compositions obtained from whole cell lysates is conserved from bacteria to Homo sapiens, and resembles that calculated from complete genomes. This basic pattern is characterized by a “star-shape” that changes slightly among species, and changes in amino acid composi-tion seem to reflect biological evolution. 5) Organisms can essentially be classified according to two codon patterns. Biological evolution due to nucleotide sub-stitutions can be expressed by simple linear formulas based on mathematical principles, while natural selection must affect species pre- servation after nucleotide alternations. There-fore, although Darwin’s natural selection is not directly involved in nucleotide alternations, it contributes obviously to the selection of nu-cleotide alternations. Thus, Darwin’s natural selection is doubtless an important factor in biological evolution.

DCHA AS A NEW REAGENT FOR THE ESTERIFICATION OF OBSTINATED AMINO ACIDS BY THE MERRIFIELD'S RESIN

The obstinated amino acid,Boc-Asn(or Boc-Gln),was directly anchored onto the Merrifield's resin using DCHA as the base in present reaction.The yield(71.88%)of Boc-Asn-OCH_2-resin was much better than those(0-33.5%)using Cs_2CO_3,KOH,KF.DEA and TEA as the base.which are efficient reagents for other amino acids in the same reaction.

Recent progress in the applications of presynaptic dopaminergic positron emission tomography imaging in parkinsonism

Nowadays,presynaptic dopaminergic positron emission tomography,which assesses deficiencies in dopamine synthesis,storage,and transport,is widely utilized for early diagnosis and differential diagnosis of parkinsonism.This review provides a comprehensive summary of the latest developments in the application of presynaptic dopaminergic positron emission tomography imaging in disorders that manifest parkinsonism.We conducted a thorough literature search using reputable databases such as PubMed and Web of Science.Selection criteria involved identifying peer-reviewed articles published within the last 5 years,with emphasis on their relevance to clinical applications.The findings from these studies highlight that presynaptic dopaminergic positron emission tomography has demonstrated potential not only in diagnosing and differentiating various Parkinsonian conditions but also in assessing disease severity and predicting prognosis.Moreover,when employed in conjunction with other imaging modalities and advanced analytical methods,presynaptic dopaminergic positron emission tomography has been validated as a reliable in vivo biomarker.This validation extends to screening and exploring potential neuropathological mechanisms associated with dopaminergic depletion.In summary,the insights gained from interpreting these studies are crucial for enhancing the effectiveness of preclinical investigations and clinical trials,ultimately advancing toward the goals of neuroregeneration in parkinsonian disorders.

Analysis of the N Protein Sequence Variability in 13 Isolated PRRSV Strains from China

Object: To analyze porcine reproductive and respiratory syndrome virus (PRRSV) strains from 13 infection cases via the N protein gene and its encoded amino acid sequence and to provide a theoretical basis for the epidemiological study, prevention and control of porcine reproductive and respiratory syndrome (PRRS). Methods: In clinically suspected PRRSV infections, viruses were isolated by extracting viral nucleic acid and amplifying the N protein gene by RT-PCR. Then, the product was purified and sequenced to acquire the whole gene sequence of the N protein and its encoded amino acid sequence. DNASTAR software was used to analyze the homology, the genetic evolution and the derivation of the variability of amino acids of the N protein gene from 13 PRRSV strains and classical domestic and foreign strains. Results: Among the thirteen strains of PRRSV isolated from this study, ten strains had the greatest homology with the JXA1 strain (98.9% - 100%), and they belonged to the sublineage 8.7. The remaining three strains had the greatest homology with the NADC30 strain (95.4% - 97.1%), and they belonged to lineage one. The analysis of the variability of N protein amino acids showed that there were high frequency mutations in the five loci of 13 isolated strains of PRRSV as follows: 15th amino acid (10/13), 46th amino acid (11/13), 91st amino acid (10/13), 109th amino acid (10/13), and 117th amino acid (10/13). Conclusion: In recent years, sublineage 8.7 was the dominant pedigree in field PRRSV epidemic strains in China with lineage one occupying a certain proportion of the field. Four high frequency mutations existed in N protein antigen epitopes of isolated strains from the region. The nuclear localization signal (NLS) structure, specifically the 46th amino acid residue of the N protein, was mutated and genetically stable.

Free amino acid content in trunk,branches and branchlets of Araucaria angustifolia(Araucariaceae)

Araucaria angustifolia(Bertol.) O. Kuntze exhibits dimorphism in its stem structure, where the trunk is orthotropic and branches and branchlets(primary and secondary branches) are plagiotropic. These stems exhibit different behavior when used for vegetative propagation,and only segments of trunk can form a complete plant. The physiological and biochemical mechanisms that characterize these stems are still little known. The aim of this study was to describe the free amino acid profiles in trunks,branches, and branchlets of A. angustifolia. Segments of 5 cm in length were excised from young individuals below the stem apex. The needles were removed and samples were frozen and lyophilized. The determinations were made by high-performance liquid chromatography, and the results were expressed as lg/g fresh weight(FW). The trunks and branches had the highest content of total amino acids, which were 112.23 ± 20.57 lg/g FW and 111.97 ± 27.78 lg/g FW, respectively. The amino acids—glutamine, aspartate and c-aminobutyric acid and tyrosine—were noticeably higher in the three types of stems.In the trunk, a higher amount of asparagine and tryptophan,was also detected. Glutamic acid and glutamine were found in higher quantities in the branches. The branchlets had very low total amino acid content (30.79 ± 4.19 lg/g FW), wherein asparagine is the only amino acid not detected. Thus, it was observed that the profile of the free amino acid differs among trunks, branches, and branchlets in A. angustifolia, indicating that they perform different functions.

Synthesis,Characterization and Structure of Chiral Amino Acids and Their Corresponding Amino Alcohols with Camphoric Backbone

Chiral amino acids and their corresponding amino alcohols bearing camphoric backbone were prepared from D-（＋）-camphoric imide and characterized by infrared, elemental analysis, ESI-MS, and NMR measurements. Among them, one intermediate （1S,3R）-3-amino-2,2,3- trimethyl cyclopentane-1-carboxylic acid hydrochloride 3 was structurally elucidated by X-ray diffraction techniques. Versatile intermolecular hydrogen bonding interactions observed in its packing structure result in a two-dimensional framework.

Natural selection in vertebrate evolution under genomic and biosphere biases based on amino acid content: Primitive vertebrate hagfish (<i>Eptatretus burgeri</i>)

Cluster analyses using the amino acid content predicted from the coding regions (13 genes) of complete vertebrate mitochondrial genomes as traits grouped selected vertebrates into two clusters, terrestrial and aquatic vertebrates. Exceptions were the hagfish (Eptatretus burgeri), thought to be an early ancestor of vertebrates, and the black spotted frog (Rana nigromaculata), which is terrestrial as an adult and aquatic as a larva. These two species fall into the terrestrial and aquatic clusters, respectively. Using the nucleotide (G, C, T and A) content in the coding and non-coding regions, and in the complete genome as traits, similar results were obtained but with some additional exceptions. In addition, phylogenetic analyses of 16S rRNA sequences produced a consistent result. The results of this study indicated that vertebrate evolution is controlled by natural selection under both an internal bias as a result of nucleotide replacement genomic rules, and an external bias caused by environmental biospheric conditions.

Rapid, accurate and serotype independent pipeline for in silico epitope mapping of SARS-CoV-2 antigens: a combined machine learning and Chou’s pseudo amino acid composition method

Here,a new integrated machine learning and Chou’s pseudo amino acid composition method has been proposed for in silico epitope mapping of severe acute respiratorysyndrome-like coronavirus antigens.For this,a training dataset including 266 linear B-cell epitopes,1,267 T-cell epitopes and 1,280 non-epitopes were prepared.The epitope sequences were then converted to numerical vectors using Chou’s pseudo amino acid composition method.The vectors were then introduced to the support vector machine,random forest,artificial neural network,and K-nearest neighbor algorithms for the classification process.The algorithm with the highest performance was selected for the epitope mapping procedure.Based on the obtained results,the random forest algorithm was the most accurate classifier with an accuracy of 0.934 followed by K-nearest neighbor,artificial neural network,and support vector machine respectively.Furthermore,the efficacies of predicted epitopes by the trained random forest algorithm were assessed through their antigenicity potential as well as affinity to human B cell receptor and MHC-I/II alleles using the VaxiJen score and molecular docking,respectively.It was also clear that the predicted epitopes especially the B-cell epitopes had high antigenicity potentials and good affinities to the protein targets.According to the results,the suggested method can be considered for developing specific epitope predictor software as well as an accelerator pipeline for designing serotype independent vaccine against the virus.

Proteolipid protein 1 gene sequencing of hereditary spastic paraplegia

PCR amplification and sequencing of whole blood DNA from an individual with hereditary spastic paraplegia, as well as family members, revealed a fragment of proteolipid protein 1 （PLP1） gene exon 1, which excluded the possibility of isomer 1 expression for this family. The fragment sequence of exon 3 and exon 5 was consistent with the proteolipid protein 1 sequence at NCBI. In the proband samples, a PLP1 point mutation in exon 4 was detected at the basic group of position 844, T→C, phenylalanine→leucine. In proband samples from a male cousin, the basic group at position 844 was C, but gene sequencing signals revealed mixed signals of T and C, indicating possible mutation at this locus. Results demonstrated that changes in PLP1 exon 4 amino acids were associated with onset of hereditary spastic paraplegia.

Effect of Lycopus lucidus Turcz.supplementation on gut microflora and short chain fatty acid composition in Crj:CD-1 mice

We investigated the diversity and composition of microflora in feces of Lycopus lucidus Turcz.-fed mice.In addition,we evaluated the production of major cytokines(Interleukin-6 and-10)which are related to inflammation and fatty acid composition of several tissues.16S ribosomal DNA sequencing-based microbiome taxonomic profiling analysis was performed utilizing the EzBioCloud data base.Male mice fed on L.lucidus showed a significantly reduced number of lactic acid bacteria and coliform in the feces compared with the control group(p<0.05).16S rDNA sequencing analysis of fecal samples showed that L.lucidus supplementation decreased the community of harmful microflora(Enterobacteriaceae including Escherichia coli and Bacteroides sp.)in feces compared with the control group(p<0.05).There were no significant differences in mRNA expression of cytokine IL-6 and IL-10 between the control and L.lucidus fed groups.The fecal fatty acid composition in the L.lucidus group had percentages of 4:0,6:0,8:0 and 10:0 in the intestine but those short chain fatty acids were not detected in the control group.Our results showed that L.lucidus supplementation influenced gut environment by decreasing harmful microflora and increased the percentages of several short fatty acids.

Protective effects of tilapia(Oreochromis niloticus)skin gelatin hydrolysates on osteoporosis rats induced by retinoic acid

Tilapia skin gelatin hydrolysates(TSGH)were obtained by complex protease hydrolysis.The amino acid sequences of 50 peptides in TSGH were identified,and most of these peptides were found to contain the-Gly-Pro-sequence.The osteoporosis(OP)rat model induced by retinoic acid was prepared,and the effects of different doses of TSGH on OP in vivo were evaluated.Serum calcium(Ca)and phosphate(P),alkaline phosphatase activity,and osteocalcin levels in OP rats were regulated by TSGH.The bone length,dry weight index,maximum load,and Ca content of OP rats significantly increased by treatment TSGH in a dosedependent manner.Micro-CT images of the femurs and tibias of the rats indicated that the bone mineral density,cortical bone thickness,and cortical/trabecular bone area ratios were recovered and that OP symptoms were improved.Tartrate-resistant acid phosphate and hematoxylin-eosin staining showed that osteoclast numbers and histomorphological changes in the femurs in OP rats could be recovered by TSGH.

工业大麻CsIAA1基因克隆及表达分析

研究以工业大麻云麻7号(Y7)为材料,克隆CsIAA1(Auxin-responsive protein IAA1)基因,通过生物信息学分析CsIAA1序列特征,经RT-qPCR研究CsIAA1组织特异性表达模式;结果表明,CsIAA1基因的CDS全长为621 bp,编码了206个氨基酸,含AUX_IAA保守结构域,属于不稳定蛋白;系统进化分析可知,工业大麻CsIAA1与糙叶山黄麻、东山麻等亲缘关系较近;通过烟草叶片瞬时表达和共聚焦试验得知,CsIAA1基因定位在细胞核中;通过RT-qPCR分析发现,在外源IAA处理12 h内,CsIAA1在1 h时快速响应生长素的处理,表达量最高;在工业大麻雄蕊不同发育阶段中,发育初期表达量比发育期和盛花期要高,且随着发育的进行呈逐渐下降趋势,推测CsIAA1参与调控工业大麻雄蕊发育;该研究从工业大麻中克隆出生长素响应基因CsIAA1并对其进行生信和表达分析,为后续探究工业大麻性别发育机制奠定了研究基础.

Isolation and Characterization of SARS-CoV-2 in Kenya

The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected individuals across the world, evolving into the COVID-19 pandemic. Notably, early signs of the virus’s existence were observed in various countries before the initial outbreak in Wuhan. As of 12th of April, the respiratory disease had infected over 762 million people worldwide, with over 6.8 million deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is the isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction was conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). Genome sequencing revealed the circulation of two isolates that share a close relationship with the Benin isolate with the D614G common mutation identified along the S protein. These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region.