Search

BackgroundHIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data.MethodsWe simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively.ResultsConsensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network.ConclusionSource attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.

Abstract Background Structural variations play a significant role in genetic diseases and evolutionary mechanisms. Extensive research has been conducted over the past decade to detect simple structural variations, leading to the development of well-established detection methods. However, recent studies have highlighted the potentially greater impact of complex structural variations on individuals compared to simple structural variations. Despite this, the field still lacks precise detection methods specifically designed for complex structural variations. Therefore, the development of a highly efficient and accurate detection method is of utmost importance. Result In response to this need, we propose a novel method called FindCSV, which leverages deep learning techniques and consensus sequences to enhance the detection of SVs using long-read sequencing data. Compared to current methods, FindCSV performs better in detecting complex and simple structural variations. Conclusions FindCSV is a new method to detect complex and simple structural variations with reasonable accuracy in real and simulated data. The source code for the program is available at https://github.com/nwpuzhengyan/FindCSV .

Background: Structural variations play a significant role in genetic diseases and evolutionary mechanisms. Extensive research has been conducted over the past decade to detect simple structural variations, leading to the development of well-established detection methods. However, recent studies have highlighted the potentially greater impact of complex structural variations on individuals compared to simple structural variations. Despite this, the field still lacks precise detection methods specifically designed for complex structural variations. Therefore, the development of a highly efficient and accurate detection method is of utmost importance. Result: In response to this need, we propose a novel method called FindCSV, which leverages deep learning techniques and consensus sequences to enhance the detection of SVs using long-read sequencing data. Compared to current methods, FindCSV performs better in detecting complex and simple structural variations. Conclusions: FindCSV is a new method to detect complex and simple structural variations with reasonable accuracy in real and simulated data. The source code for the program is available at https://github.com/nwpuzhengyan/FindCSV. [ABSTRACT FROM AUTHOR]

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8–10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database.

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8–10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database. [ABSTRACT FROM AUTHOR]

The reference sequences play an essential role in genome assembly, like type specimens in taxonomy. Those references are also samples obtained at some time and location with a specific method. How can we evaluate or discriminate uncertainties of the reference itself and assembly methods? Here we bootstrapped 50 random read data sets from a small circular genome of a Escherichia coli bacteriophage, phiX174, and tried to reconstruct the reference with 14 free assembly programs. Nine out of 14 assembly programs were capable of circular genome reconstruction. Unicycler correctly reconstructed the reference for 44 out of 50 data sets, but each reconstructed contig of the failed six data sets had minor defects. The other assembly software could reconstruct the reference with minor defects. The defect regions differed among the assembly programs, and the defect locations were far from randomly distributed in the reference genome. All contigs of Trinity included one, but Minia had two perfect copies other than an imperfect reference copy. The centroid of contigs for assembly programs except Unicycler differed from the reference with 75bases at most. Nonmetric multidimensional scaling (NMDS) plots of the centroids indicated that even the reference sequence was located slightly off from the estimated location of the true reference. We propose that the combination of bootstrapping a reference, making consensus contigs as centroids in an edit distance, and NMDS plotting will provide an evidential statistic way of genetic assembly for non-fragmented base sequences.

Protein phosphorylation is the most frequent post-translational modification by which the properties of eukaryotic proteins can be reversibly modified. In humans, over 500 protein kinases generate a huge phosphoproteome including more than 200,000 individual phosphosites, a figure which is still continuously increasing. The in vivo selectivity of protein kinases is the outcome of a multifaceted and finely tuned process where numerous factors play an integrated role. To gain information about the actual contribution to this process of local features that reflect the interaction of the protein targets with the catalytic site of the kinases, the prevalence of the commonest motifs determining the consensus sequence of Ser/Thr-specific kinases has been examined in the whole human phosphoproteome and in the phosphoproteomes generated by a panel of the 47 most pleiotropic protein kinases. Our analysis shows that: (1) most phosphosites do conform to at least one of the motifs considered, with a substantial proportion conforming to two or more of them; (2) some motifs, with special reference to the one recognized by protein kinase CK2 (pS/pT-x-x-E/D) are very promiscuous, being abundantly represented also at the phosphosites of all the other protein kinases considered; (3) by contrast, other phosphorylated motifs, notably pS/pT-P, pS/pT-Q and pS-x-E, are more discriminatory and selective, being nearly absent in the phosphosites that are not attributable to certain categories of kinases. The information provided will prove helpful to make reliable inferences based on the manual inspection of individual phosphosites. [ABSTRACT FROM AUTHOR]

BackgroundMultiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. However, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation.ResultsWe introduce ProfileGrids that represent a multiple sequence alignment as a matrix color-coded according to the residue frequency occurring at each column position. JProfileGrid is a Java application for computing and analyzing ProfileGrids. A dynamic interaction with the alignment information is achieved by changing the ProfileGrid color scheme, by extracting sequence subsets at selected residues of interest, and by relating alignment information to residue physical properties. Conserved family motifs can be identified by the overlay of similarity plot calculations on a ProfileGrid. Figures suitable for publication can be generated from the saved spreadsheet output of the colored matrices as well as by the export of conservation information for use in the PyMOL molecular visualization program. We demonstrate the utility of ProfileGrids on 300 bacterial homologs of the RecA family – a universally conserved protein involved in DNA recombination and repair. Careful attention was paid to curating the collected RecA sequences since ProfileGrids allow the easy identification of rare residues in an alignment. We relate the RecA alignment sequence conservation to the following three topics: the recently identified DNA binding residues, the unexplored MAW motif, and a unique Bacillus subtilis RecA homolog sequence feature.ConclusionProfileGrids allow large protein families to be visualized more effectively than the traditional stacked sequence alignment form. This new graphical representation facilitates the determination of the sequence conservation at residue positions of interest, enables the examination of structural patterns by using residue physical properties, and permits the display of rare sequence features within the context of an entire alignment. JProfileGrid is free for non-commercial use and is available from . Furthermore, we present a curated RecA protein collection that is more diverse than previous data sets; and, therefore, this RecA ProfileGrid is a rich source of information for nanoanatomy analysis.

In this study, the phenomenon of the stability-activity trade-off, which is increasingly recognized in enzyme engineering, was explored. Typically, enhanced stability in enzymes correlates with diminished activity. Utilizing Rosa roxburghii copper-zinc superoxide dismutase ( RrCuZnSOD ) as a model, single-site mutations were introduced based on a semirational design derived from consensus sequences. The initial set of mutants was selected based on activity, followed by combinatorial mutation. This approach yielded two double-site mutants, D25/A115T (18,688 ± 206 U/mg) and A115T/S135P (18,095 ± 1556 U/mg), exhibiting superior enzymatic properties due to additive and synergistic effects. These mutants demonstrated increased half-lives ( T 1/2 ) at 80 °C by 1.2- and 1.6-fold, respectively, and their melting temperatures ( T m ) rose by 3.4 and 2.5 °C, respectively, without any loss in activity relative to the wild type. Via an integration of structural analysis and molecular dynamics simulations, we elucidated the underlying mechanism facilitating the concurrent enhancement of both thermostability and enzymatic activity.

Bu çalışmada özel DNA örüntüleri için yeni ve hızlı bir sekans eşleştirme tekniği sunulmakta ve yakın geçmişte üretilen CPU mimarileri üzerinde deneysel karşılaştırmalar yapılmaktadır. Bu çalışmada, bilhassa kanser tedavisinde, önemli bir yere sahip olan P53 DNA-bağlayan konsensüs sekansı göz önüne alınmıştır. Biyolojik kazanımlara göre P53 örüntüsü farklı sekans formlarında karşımıza çıkabilmekte ve sekans uzunluğu değişebilmektedir. Bu nedenle P53 sekansının klasik sekans eşleştirme algoritmaları ile çözümü mümkün olamamaktadır. Bu çalışmada verimli çözüm yöntemi sunmak amacıyla, sınıf özellikli bit-tabanlı sekans eşleştirme algoritması göz önüne alınmıştır. Hedef doğrultusunda, 64-bit paketlenmiş değişken kullanarak yeni bir arama ve eşleştirme algoritması önerilmiştir. Örüntü sekansının değişken uzunluk gösterebilmesi nedeniyle karşılaşılması muhtemel engelleri aşmak için ise veri tabanında P53 sekansının özel kısımlarına dair aramalar yapılmıştır. Deneysel analiz için yaklaşık 2.3 milyar nükleotidden oluşan mus musculus DNA sekansı seçilmiştir. Karşılaştırılan algoritmalar üç farklı bilgisayar mimarisinde test edilmiştir. Deneysel sonuçlar, geliştirdiğimiz algoritmanın P53 sekans arama konusunda tüm mimari platformlarında en iyi verimliliği sağladığını göstermektedir. Yapısı gereği bu algoritma, benzer sekans eşleştirme problemlerinin çözümünde de verimli olanaklar sunmaktadır.

We present a novel fast string matching technique for special DNA pattern forms and compare performance of recent CPU architectures on the matching problem. In particular, we consider consensus P53 DNA-binding consensus sequence, which has an important contribution for cancer treatment. Based on biological findings, consensus P53 pattern may emerge in various sequence forms and its length is not deterministic. Therefore, classic string matching algorithms are not able to solve the problem. For efficient solution, we consider bitwise string matching algorithms with classes and present a novel search technique which is based on 64-bit packed variables. In order to prevent obstacles based on variable length of the pattern, we search specific indexes of P53 on databases. For experimental analysis, we make use of mus musculus DNA sequences with approximately 2.3 billion nucleotides. We compare algorithm performance and three architectures with various level CPU parallelism. Test results show that our technique presents search efficiency during P53 pattern search in each architecture platform. Due to its structure, the algorithm also introduces an efficient solution to similar string matching with class problems.

A nuclear export signal (NES) is a protein localization signal, which is involved in binding of cargo proteins to nuclear export receptor, thus contributes to regulate localization of cellular proteins. Consensus sequences of NES have been used to detect NES from protein sequences, but suffer from poor predictive power. Some recent peering works were proposed to use biochemical properties of experimental verified NES to refine NES candidates. Those methods can achieve high prediction rates, but their execution time will become unacceptable for large-scale NES searching if too much properties are involved. In this work, we developed a novel computational approach, named NES-REBS, to search NES from protein sequences, where biochemical properties of experimental verified NES, including secondary structure and surface accessibility, are utilized to refine NES candidates obtained by matching popular consensus sequences. We test our method by searching 262 experimental verified NES from 221 NES-containing protein sequences. It is obtained that NES-REBS runs in 2-3mins and performs well by achieving precision rate 47.2% and sensitivity 54.6%. [ABSTRACT FROM AUTHOR]

A vast amount of sequence data has been generated due to advancements in DNA sequencing technology. This exponential increase requires new and efficient methods for the analysis of DNA sequence data. Predicting genes in this newly sequenced data is an important and essential step towards genome annotation. Genome annotation helps in determining function of these genes. Accurate splice site prediction in DNA sequences leads to correct gene structure prediction in eukaryotes and it requires effective modelling of regions surrounding these sites. A large number of methods for splice site prediction are available in literature but very few of them are suitable to be incorporated as gene prediction module because of their complexity. In this paper, a splice site prediction method based on second order markov model and support vector machine is developed. This method shows improvement over most of the existing splice site predictors in use today. The experimental results suggest that second order markov model is an effective pre-processing approach. This approach when combined with support vector machine provides better classification accuracy in predicting splice sites. [ABSTRACT FROM AUTHOR]

Cherry tomatoes (Lycopersicon esculentum var. cerasiforme) is the main tomato variety planted in Hainan Province, China and is prized for its nutritional value and sweet taste (Zheng et al. 2020). During October 2020 to February 2021, a leaf spot disease was observed on cherry tomatoes (cultivar Qianxi) in Chengmai, Hainan Province. The disease incidence was approximately 40% in each of three fields in Yongfa (19°76'-21°08'N, 110°21'-110°51'E). Leaves were initially chlorotic before developing black, irregular-shaped lesions on the leaf margins or tips. After several days, lesions expanded along the mid-vein to encompass the entire leaf. Then, the affected leaves turned gray-brown, leading to defoliation. Severely affected leaves became dry and necrotic. Leaf tissues of 10 diseased plants samples collected from the fields were surface sterilized in 70% ethanol for 30 s, 0.1% HgCl2 for 30 s, rinsed thrice with sterile distilled water for 30 s, placed on a modified potato dextrose agar (PDA) with 30 mg/liter of kanamycin sulfate, and incubated at 28°C in the dark for 3 to 5 days. Three fungal isolates were obtained from the diseased leaves by single-sporing. The mycelia on PDA were white and later became gray or dark gray after 3 to 4 days. Conidia were rostrate, straight to slightly curved, ellipsoidal to narrowly obclavate, dark brown, protuberant with a darker and thicker wall at the basal end. Conidia were 4 to 12 distoseptate and measured 63.92 ± 5.77 × 13.47 ± 1.22 µm (n= 50) Conidiophores were single, cylindrical, dark brown, geniculate, with swollen conidiogenous cells containing a acircular conidial scar. Morphological characteristics of the isolates were similar to those of Exserohilum rostratum (Cardona et al. 2008). A representative isolate (FQY-7) was used for pathogenicity and genomic studies. Genomic DNA was extracted from the mycelium of a representative isolate (FQY-7). The internal transcribed spacer (ITS) region, actin (act), translation elongation factor 1-alpha (tef1-α), glyceraldehydes 3-phos-phate dehydrogenase (gapdh) and β-tubulin (tub2) genes were amplified with primers ITS1/ITS4 (White et al. 1990), Act1/Act4 (Voigt and Wöstemeyer 2000), EF1-728F/EF1-986R (Carbone and Kohn 1999), Gpd-1/Gpd-2 (Berbee et al. 1999) and T1 (O'Donnell and Cigelnik 1997) + Bt2b (Glass and Donaldson 1995). The consensus sequences (GenBank Accession No. MW036279 for ITS, MW133266 for act, MW133268 for tef1-α, MW133267 for gapdh, and MW133269 for tub2) were aligned using BLAST in GenBank obtaining 100%, 100%, 99%, 100%, and 99% identity to E. rostratum strain CBS706 (LT837842, LT837674, LT896663, LT882546, LT899350). Maximum likelihood analysis based on the combined five gene sequences was conducted under 1,000 bootstrap replicates. The Phylogenetic tree showed that FQY-7 and E. rostratum were located in one clade supported with 99% bootstrap values. Pathogenicity test was performed by depositing 10-µl droplets of a conidial suspension (1 × 106 per ml) into 5 noninoculated leaves (using a sterile needle) of 10 healthy 5-month-old cherry tomato (cv. Qianxi) plants. An equal number of artificially control leaves were received only sterile water to serve as a negative control. The test was conducted three times. Plants were kept at 28°C with 80% humidity and observed for symptoms every day. Two weeks after inoculation, all the inoculated plants showed symptoms of black spots similar to those observed in the field. No symptoms were observed on the controls. FQY-7 was successfully re-isolated from the inoculated leaves and confirmed by morphological characterization and molecular assays as described herein. To the best of our knowledge, this is the first report of leaf spot of cherry tomatoes caused by E. rostratum in China. Confirming the existence of this pathogen in this area will be useful to adopt effective field management measures to control this disease on cherry tomatoes. References: Berbee, M. L., et al. 1999. Mycologia 91:964. Cardona, R. et al. 2008. Bioagro 20:141. Carbone, I. and Kohn, L. M. 1999. Mycologia 91:553. Glass, N. L., and Donaldson, G. C. 1995. Appl. Environl. Microb. 61:1323. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA. O'Donnell K., and Cigelnik, E. 1997. Mol. Phylogenet. Evol. 7:103. Voigt, K., and Wöstemeyer, J. 2000. Microbiol. Res. J. 155:179. Zheng J., et al. 2020. Guangdong Agr. Sci. 47:212. The author(s) declare no conflict of interest.

The advent of advanced NGS technologies have led to the generation of enormous amount of sequence data which further aid in the discovery of the various type of markers such as SSRs, SNPs, InDels, etc. Among all these markers, microsatellite SSR markers can be mined from the ddRADseq data as certain properties of SSR markers make them ideal markers for study. These assist researchers and breeders in diversity analysis and producing new varieties with desired traits. To extract the markers, first, the ddRADseq data is assembled into consensus sequences using STACKS program which are further assembled for mining microsatellites using QDD along with MISA tool., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Transposable elements (TEs) exert an increasingly diverse spectrum of influences on eukaryotic genome structure, function, and evolution. A deluge of genomic, transcriptomic, and proteomic data provides the foundation for turning essentially any non-model eukaryotic species into an emerging model to study any and all aspects of organismal biology, ultimately shaping future directions for biomedical, environmental, and biodiversity research. However, identification and annotation of the mobile genome component still lags behind the standards accepted for host gene annotation. To achieve the objective of providing every genome project with a comprehensive description of its mobilome component in addition to the standard genic and transcriptomic datasets, each step of TE identification, classification, and annotation should be focused on improving TE boundary designation, reducing identification error rates, and providing accurate information on the type and integrity of TE insertions. Here, we offer practical advice for generating TE models in de novo assemblies for non-model organisms, provide step-by-step instructions to guide inexperienced TE annotators through some of the commonly utilized TE analysis pipelines, and entertain suggestions for tool improvement which could be implemented by interested developers., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Background Hepatitis B (HB) is an important disease worldwide. Almost 350 million people are positive for Hepatitis B virus surface antigen (HBsAg), and one-third of them live in China. According to a nation-wide serosurvey in China in 2006, the prevalence of HBsAg was higher in Northwest China than in other areas. However, the epidemic HBV strains in this area are poorly studied. Results In this study, 242 complete hepatitis B virus (HBV) genome sequences were obtained from HBV asymptomatic carriers in major cities of Northwest China. The 242 HBV sequences clustered into genotypes B, C and D. Through comparison of the genotype consensus sequences, 158 genotype-dependent positions were observed in P, S and X ORFs. Clinically relevant mutation screening in this study revealed that no HBV antiviral drug resistance mutations were observed and the vaccination failure mutations were heavily underrepresented. Conclusions The role of genotype D strains in HBV prevalence should not be ignored in Northwest China. Due to low prevalence of vaccination failure mutations, it can be inferred that the genotype B, C and D strains in Northwest China may have less likelihood of vaccine escape. [ABSTRACT FROM AUTHOR]

Betulaceae, with 120-150 species in six genera, are a family of Fagales that occurs mainly in the Northern Hemisphere. Previous studies of the evolution of Alnus, Betula, Carpinus, Corylus, Ostrya and Ostryopsis have relied on a relatively small number of sequence data and molecular clocks with fixed-point calibrations. We exploited Gen Bank to construct Betulaceae matrices of up to 900 sequence accessions and 9300 nucleotides of nuclear and plastid DNA; we also computed species consensus sequences to build 46- and 29-species matrices that strike a balance between species sampling and nucleotide sampling. Trees were rooted on Ticodendraceae and Casuarinaceae, and divergence times were inferred under relaxed and strict molecular clocks, using alternative fossil constraints. The data support the traditional two subfamilies, Betuloideae ( Alnus, Betula) and Coryloideae, and show that Ostryopsis is sister to Ostrya/ Carpinus. The fossil record and molecular clocks calibrated with alternating fossils indicate that the stem lineage of Betulaceae dates back to the Upper Cretaceous, the two subfamilies to the Palaeocene and the most recent common ancestors of each of the living genera to the mid- to late Miocene. A substitution rate shift in Coryloideae between 25 and 15 Mya preceded the mid- Miocene climatic optimum and may be linked to temperate niches that became available following the mid-Miocene. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 465-477. [ABSTRACT FROM AUTHOR]

Abstract: Nine endogenous Brevidensovirus-like elements (EBreVE) were identified in redclaw freshwater crayfish Cherax quadricarinatus from different sources suggesting that these elements are widespread in redclaw in northern Queensland, Australia. These endogenous virus-like elements shared nucleotide identities (70–100%) and amino acid similarities (34–100%) with infectious hypodermal and haematopoietic necrosis virus (IHHNV) scientifically classified as Penaeus stylirostris densovirus (PstDNV). They may not have originated from IHHNV genomes, but could be derived from another uncharacterised member of the genus Brevidensovirus that share nucleotide similarities with IHHNV. The most striking feature of EBreVEs was that in each case, the segment (portion) of viral sequences inserted into the host genomes was from the same region of the viral genome and most likely derived from non-structural protein regions of ancestral virus, but they cannot be assembled into one consensus sequence. The EBreVEs may be inserted into the redclaw genomes following chronic or persistent infection by a corresponding virus that may have occurred as multiple independent integration events years ago leading to the accumulation of several integrated elements in their genomes. Histological examination and polymerase chain reaction (PCR) suggested that these insertions may have a protective function to their host. [Copyright &y& Elsevier]

Abstract: The transcriptional fusion of reporter lacZ gene with cusRS regulatory promoter of cus operon of Klebsiella pneumoniae enabled us to analyze the inductive effect of copper on promoter via lacZ assay. The stimulus response curve of promoter to a range of copper metal concentrations indicated a normal sigmoidal response profile with apparent Hill coefficient 1.0. There was a positive correlation of promoter response to the increasing concentration of copper in the medium. AC50 value of copper was calculated to be 1mM, whereas the promoter response was exponential beyond 1mM and up to 2.5mM concentration. The promoter activity did not increase exponentially in copper concentration higher than 2.5mM. The promoter PcusRS requires two chromosomally encoded regulatory proteins, CusS and CusR, in trans for maximal in vitro activation. The PcusRS regulatory promoter sequence also contained regulatory −10 and −35 boxes along with CusR binding motif. The results supported the concept of cus operon regulation as an essential mechanism for maintaining the cellular homeostasis at very high (e.g. 3mM), and even toxic copper concentrations. [Copyright &y& Elsevier]

The cotton whitefly, Bemisia tabaci (Gennadius), is a cryptic species complex, and members of the complex have become serious pests in Pakistan because of their feeding and their ability to transmit cotton leaf curl virus (CLCuV). Here, an analysis was made of the identity of B. tabaci collected from cotton and a range of non-cotton hosts in the cotton-growing zones in Punjab and Sindh, the main cotton-producing provinces of Pakistan, using a portion of the mitochondrial cytochrome oxidase 1 gene. The geographic distribution of the different members of the complex was then compared with the incidence of CLCuD. Using the Dinsdale nomenclature, the results revealed three putative species, Asia 1, Asia II 1 and Middle East-Asia Minor 1. Asia II 1 (also referred to in the literature as biotypes K, P, PCG-1, PK1, SY and ZHJ2) was only recorded from Punjab cotton plants, whereas Asia 1 (also referred to in the literature as biotypes H, M, NA and PCG-2) was found in both Sindh and Punjab. Middle East-Asia Minor 1 (commonly known as biotype B and B2) was found only in Sindh. Moreover, Asia II 1 was associated with high incidences of CLCuD, whereas regions where Middle East-Asia Minor 1 was present had a lower incidence. Phylogenetic analysis showed that the Middle East-Asia Minor 1 population in Sindh formed a distinct genetic subgroup within the putative species, suggesting that the Sindh province of Pakistan may form part of its home range. So far, no individuals from the putative species Mediterranean (commonly known as biotypes Q, J and L) have been found in Pakistan. The capacity to manage pests and disease effectively relies on knowledge of the identity of the agents causing the damage. In the case of CLCuD in Pakistan, this knowledge has been obscured to some extent because of the inconsistent approach to identifying and distinguishing the different B. tabaci associated with CLCuD. The situation has now been clarified, and a strong association between disease incidence and vector identity and abundance has been shown. Given this advance, future research can now focus on factors that influence the capacity of different vector species to transmit the viruses that cause CLCuD, the reason for differences in vector abundance and the lack of geographic overlap between the cryptic vector species. This knowledge will contribute to the development of improved methods with which to manage the disease in Pakistan. Copyright © 2010 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Abstract: The statistical properties of the size distribution of DNA segments separating identical oligonucleotides are studied. For representative eukaryotes (Homo sapiens, Mus musculus, Saccharomyces cereviciae, Oryza sativa, Arabidopsis thaliana) we have demonstrated the existence of long-range correlations for the distances separating oligonucleotides of sizes 4, 5 and 6, which carry a promoter signature. This observation is independent of the consensus sequence used by the organism, as in the case of O. sativa (which mainly uses the CG promoter box) and A. thaliana (which mainly uses the TATA promoter box). If we use two parameters to characterise the size distribution separating oligonucleotides, we observe that oligonucleotides containing promoter signatures cluster together, away from the others. [Copyright &y& Elsevier]

Abstract: To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the −10 consensus region sequence and five variants forming the −10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength. [Copyright &y& Elsevier]

A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244 bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8 kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species. [Copyright &y& Elsevier]

After the finding of the involvement of the C-terminal moieties of tubulin subunits in the interaction of MAPs, different studies have focused on the substructure of the binding domains for the different MAPs. Current biochemical evidence point to the role of a low-homology sequence between α and β-subunits within the conserved region of the C-terminal domain of tubulin, in the binding of AMP-2 and tau. Another line of studies indicates that a site for interaction of the high molecular weight MAPs is located in the variable region defined by the glutamic-rich C-terminus of β-tubulin. Here, we report the usefulness of idiotypic site-directed antibodies, produced by immunization with peptides from different β-tubulin isoforms, to study both MAP-1 and MAP-2 binding sites on tubulin. On the basis of these results with site-specific antibodies along with previous structural information (Cross et al. 1991, Biochemistry 30: 4362-4366), we propose the role of consensus sequences, from the invariant β-tubulin C-terminal domain in the binding of MAP-2 and from the variable domain in the interactions of MAP-1 and MAP-2. [ABSTRACT FROM AUTHOR]

The existing classification of human Alu sequences is revised and expanded using a novel methodology and a larger set of sequence data. Our study confirms that there are two major Alu subfamilies, Alu-J and Alu-S. The Alu-S subfamily consists of at least five distinct subfamilies referred to as Alu-Sx, Alu-Sq, Alu-Sp, Alu-Sc, and Alu-Sb. The Alu-Sp and Alu-Sq subfamilies have been revealed by this study. Alu subfamilies differ from one another in a number of positions called diagnostic. In this paper the diagnostic positions are defined in quantitative terms and are used to evaluate statistical significance of the observed subfamilies. Each Alu subfamily most likely represents pseudogenes retroposed from evolving functional source Alu genes. Evidence presented in this paper indicates that Alu-Sp and Alu-Sc pseudogenes were retroposed from different source genes, during overlapping periods of time, and at different rates. Our analysis also indicates that the previously identified Alu-type transcript BC200 comes from an active Alu gene that might have existed even before the origin of dimeric Alu sequences. The source genes for Alu pseudogene families are reconstructed. It is assumed that diagnostic differences between reconstructed source genes reflect mutations that have occurred in true source Alu genes under natural selection. Some of these mutations are compensatory and are used to reconstruct a common secondary structure of Alu RNAs transcribed from the source genes. The biological function of Alu RNA is discussed in the context of its homology to the elongation-arresting domain of 7SL RNA. Practical implications of our analyses for studies of the human and of other primate genomes are outlined. A computer program that identifies diagnostic bases in individual Alu repeats is designed and made available on-line. [ABSTRACT FROM AUTHOR]

DNA sequences of the human, mouse, and rabbit immunoglobulin kappa-gene (J-C regions) are compared with respect to various DNA patterns, including dyad symmetry pairings, runs of nucleotides, repeat clusters, and repeats that occur with unusually high frequency. The significant dyad symmetry pairings within each of the sequences emphasize the two 'control-enhancer' elements of the J-C intron. Dyad symmetry pairs between the J-C region and a number of kappa variable (V)-gene domains suggest differences in the affinities between the V and J segments. It is the 'consensus heptamer' rather than the 'consensus nonamer' that embodies the longest V-J dyad symmetry combinations. In the rabbit there are long runs and repeat clusters of the sequences that identify regions of high duplication; these regions are absent in the human and mouse sequences. High-frequency oligonucleotides feature the consensus nonamer 5′ to the J segments, especially in the mouse sequence. [ABSTRACT FROM AUTHOR]

In extremely cold environments, living organisms like plants, animals, fishes, and microbes can die due to the intracellular ice formation in their bodies. To sustain life in such cold environments, some cold-blooded species produced Antifreeze proteins (AFPs), also called ice-binding proteins. AFPs are not only limited to the medical field but also have diverse significance in the area of biotechnology, agriculture, and the food industry. Different AFPs exhibit high heterogeneity in their structures and sequences. Keeping the significance of AFPs, several machine-learning-based models have been developed by scientists for the prediction of AFPs. However, due to the complex and diverse nature of AFPs, the prediction performance of the existing methods is limited. Therefore, it is highly indispensable for researchers to develop a reliable computational model that can accurately predict AFPs. In this connection, this study presents a novel predictor for AFPs, named AFP-CMBPred. The sequences of AFPs are formulated via four different feature representation methods, such as Amphiphilic pseudo amino acid composition (Amp-PseAAC), Dipeptide Deviation from Expected Mean (DDE), Multi-Blocks Position Specific Scoring Matrix (MB-PSSM), and Consensus Sequence-based on Multi-Blocks Position Specific Scoring Matrix (CS-MB-PSSM) to collect local and global descriptors. In the next step, the extracted feature vectors are evaluated via Support Vector Machine (SVM) and Random Forest (RF) based classification learners. The prediction performance of both classifiers is further assessed using three validation methods i.e., jackknife test, 10-fold cross-validation test, and independent test. After examining the prediction rates of all validation tests, it was found that our proposed model achieved the higher prediction accuracies of ∼2.65%, ∼2.84%, and ∼3.37% using jackknife, K-fold, and independent test, respectively. The experimental outcomes validate that our proposed "AFP-CMBPred" predictor secured the highest prediction results than the existing models for the identification of AFPs. It is further anticipated that our proposed AFP-CMBPred model will be considered a valuable tool in the research academia and drug development., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Specific motifs in the genomes of the Chlamydiaceae family have been sought. The quest for reliable and convenient genetic markers for identification and typing of bacteria remains an urgent task for current molecular biology. Progress in sequencing has resulted in complication of the database of complete genomic bacteria nucleotide sequences. This has made it possible to seek and select genetic targets for identification and genotyping of bacteria based on direct comparative analysis of complete genomic sequences. The current study compares the genomes of the members of the Chlamydiaceae family with the aim of revealing specific nucleotide motifs that could serve as genetic markers of this family. A search for consensus fragments was performed using the Visual Basic for Application software for MS Excel. Complete coincidence of fragments with 25 nucleotide length in the compared genomes was used as the criterion for consensus sequence selection. One complete genomic sequence for each member of eight Chlamydiaceae species was investigated. The experimental set did not include the complete sequence of C. suis since it was missing in the GenBank database for the moment of investigation. Comparison of C. trachomatis genome with other members of the Chlamydiaceae family succeeded in revealing 41 motifs common for all eight investigated Chlamydia species. The highest number of consensus motifs was revealed in ribosomal RNA genes and in tRNA genes. In addition to in rRNA and tRNA genes, consensus motifs were found in five genes and six intergene regions. The consensus motifs in the CTL0299, CTL0800, dagA, and hctA genes detected in the present study may be considered as candidate regions for identification of the Chlamydiaceae family species. [ABSTRACT FROM AUTHOR]

The goal of protein design is to create proteins that are stable, soluble, and active. Here we focus on one approach to protein design in which sequence information is used to create a "consensus" sequence. Such consensus sequences comprise the most common residue at each position in a multiple sequence alignment (MSA). After describing some general ideas that relate MSA and consensus sequences and presenting a statistical thermodynamic framework that relates consensus and non-consensus sequences to stability, we detail the process of designing a consensus sequence and survey reports of consensus design and characterization from the literature. Many of these consensus proteins retain native biological activities including ligand binding and enzyme activity. Remarkably, in most cases the consensus protein shows significantly higher stability than extant versions of the protein, as measured by thermal or chemical denaturation, consistent with the statistical thermodynamic model. To understand this stability increase, we compare various features of consensus sequences with the extant MSA sequences from which they were derived. Consensus sequences show enrichment in charged residues (most notably glutamate and lysine) and depletion of uncharged polar residues (glutamine, serine, and asparagine). Surprisingly, a survey of stability changes resulting from point substitutions show little correlation with residue frequencies at the corresponding positions within the MSA, suggesting that the high stability of consensus proteins may result from interactions among residue pairs or higher-order clusters. Whatever the source, the large number of reported successes demonstrates that consensus design is a viable route to generating active and in many cases highly stabilized proteins., (© 2020 Elsevier Inc. All rights reserved.)

The splice-site sequences of U2-type introns are highly degenerate, so many different sequences can function as U2-type splice sites. Using our new profiles based on hydrophobicity properties we pointed out specific properties for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes extracted from GenBank to define positions having conserved properties, namely hydrophobicity, that are potentially essential for recognition by spliceosome. GT-AG introns exist in U2 and U12-types. Therefore, intron type cannot be simply determined by the dinucleotide termini. We attempted to distinguish U2 and U12-types introns with help of hydrophobicity profiles on sets of spice sites for U2 or U12-type introns extracted from SpliceRack database. The positions given by our method, which may be important for recognition by spliceosome, were compared to the nucleotide consensus provided by a classical method, Pictogram. We showed that there is a similarity of hydrophobicity profiles inside intron types. On one hand, GT-AG and GC-AG introns belonging to U2-type have resembling hydrophobicity profiles as well as AT-AC and GT-AG introns belonging to U12-type. On the other hand, hydrophobicity profiles of U2 and U12-types GT-AG introns are completely different. We suggest that hydrophobicity profiles facilitate definition of intron type, distinguishing U2 and U12 intron types and can be used to build programs to search splice site and to evaluate their strength. Therefore, our study proves that hydrophobicity profiles are informative method providing insights into mechanisms of splice sites recognition.