National Center For Biotechnology Information Research Articles

The influence of novel coronavirus pneumonia on chronic disease management of asthma-a narrative review.

The coronavirus disease 2019 (COVID-19) pandemic has taken a huge global toll on all fronts, creating new challenges for the diagnosis and treatment of respiratory diseases. For chronic management of asthma, on the one hand, the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may affect the asthma disease itself; on the other hand, in order to control the spread of the pandemic, forced isolation, mask-wearing and various disinfection measures also have an impact on the condition and medication of asthma patients. This article reviews the changes in chronic asthma management under the COVID-19 pandemic to provide reference for chronic disease management of asthma after the pandemic and for various public health emergencies in the future. Online searching of literature was performed. The National Center for Biotechnology Information (NCBI), PubMed, Google Scholar, and EMBASE were searched. COVID-19 has had a huge impact on the world, and has also brought new challenges to the diagnosis and treatment of asthma and chronic disease management. On the one hand, the existence of the 2019 novel coronavirus directly affects the asthma disease itself, on the other hand, due to the particularity of the asthma disease itself, different levels of isolation and controls can cause patients with different degrees of medical difficulties; in addition, the application of various disinfectants in the environment also increases the risk of acute attacks of asthma patients, as well as mask-wearing, vaccination, anxiety about the disease, panic, etc., all of which have posed various degrees of impact on the condition and psychology of asthma patients. The pandemic of COVID-19 has brought many difficulties to the chronic disease management of asthma, and has had a certain impact on the disease control of asthma patients. In the era with overflowing information, internet hospital is the current trend, and there is a long way to go for effectively penetrating medical resources virtually via the internet into chronic disease management of asthma.

GeneGPT: augmenting large language models with domain tools for improved access to biomedical information.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this article, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: First, API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; second, GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; finally, different types of errors are enriched in different tasks, providing valuable insights for future improvements. The GeneGPT code and data are publicly available at https://github.com/ncbi/GeneGPT.

Molecular detection and identification of Plasmodium spp. isolated from captive-bred cynomolgus monkeys in Bogor, Indonesia

Background and Aim: Asian macaques are natural hosts of several Plasmodium species. Some monkey malaria parasites may infect humans and cause zoonotic infections. This study was conducted to estimate the prevalence of monkey malaria parasites in Bogor, Indonesia, based on molecular detection and identification, particularly in cynomolgus monkeys, which have a wide geographic distribution and share extensive habitats with humans. These data are needed to evaluate the status of simian malaria among macaques in Bogor and to study the potential risks to human health. These updated data will provide sufficient information for implementing malaria control strategies in the future and for developing a potential malaria vaccine using monkeys as an animal model. Materials and Methods: Blood samples of 274 cynomolgus monkeys (Macaca fascicularis) were collected and identified using microscopy. DNA was extracted from positive blood samples and analyzed using polymerase chain reaction (PCR) to amplify the small subunit ribosomal RNA (SSU rRNA) target gene using consensus primers for Plasmodium species. The PCR-positive samples were then nucleotide-sequenced using commercial sequencing services, analyzed using the BioEdit program, and aligned using Basic Local Alignment Search Tool from the National Center for Biotechnology Information. Phylogenetic trees were constructed using MEGA 11.0 and the neighbor-joining (NJ) method to determine the kinship of Plasmodium. Bootstrapping was performed using 500 replicates to assess the robustness of tree topologies. Results: Thirty-eight of the 274 microscopically positive samples for Plasmodium spp. were also positive using PCR, resulting in a 1640 bp amplicon. Further, analysis using nucleotide sequencing confirmed that these positive samples were Plasmodium inui with more than 99% nucleotide identity compared to GenBank sequences. Phylogenetic tree analysis of the SSU rRNA partial gene showed that all our isolates clustered and were closely related to a P. inui strain isolated from cynomolgus macaques in South China in 2011. Conclusion: P. inui is the predominant malaria parasite in cynomolgus monkeys from Bogor. Keywords: malaria, phylogenetic tree, Plasmodium inui, small subunit ribosomal RNA.

The Viability and Potential of Environmental DNA (eDNA) Detection of Freshwater Fish Based on Current Genetic Resources in Malaysia

Environmental DNA (eDNA) metabarcoding is a promising tool for regular biological monitoring, especially for freshwater fish, which are facing tremendous threats worldwide. The application of eDNA detection is a dramatic improvement on common methods of biomonitoring as it produces tangible results in a short time with low effort and little expense. However, the accuracy of the technique is largely dependent on the availability of genetic references for the target organisms. In this study, we investigated the availability of genetic resources for freshwater fish in Malaysia in three public depositories, National Center for Biotechnology Information (NCBI), Barcode of Life Data System (BOLD), and Mitochondrial Genome Database of Fish (MitoFish), focusing on seven targeted genes of mitochondrial DNA. We found that only 68.6% of freshwater fish found in Malaysia had information on at least one of the seven targeted genes, with data on Cytochrome C Oxidase Subunit I being most commonly available. Genetic information for threatened and endemic species were underrepresented (33.3%-41.7%), yet fish of commercial value and invasive species were well explored genetically. Although there is still room for improvement to achieve comprehensive and reliable genetic resource information for freshwater fish in Malaysia, the application of eDNA metabarcoding is still highly relevant. This is since the current decline in freshwater fish diversity in Malaysia is alarming and because the technique will assist in the ongoing effort to generate new genetic references for Malaysian freshwater fish.

Germination and seedling growth of groundnut seeds infected with Macrophomina phaseolina isolates

Macrophomina phaseolina is a common contaminant of groundnut (Arachis hypogaea L.) seeds but not much information has been documented about its adverse impact on seed health and germination. This study was carried out to determine the incidence of M. phaseolina on groundnut (Arachis hypogaea) seeds displayed for sale in local markets, characterize the isolates and determine how the fungal presence would affect the germination and seedling growth, so as to provide information on seed handling practices and planning strategies for reducing crop loss due to the fungus. The fungus was isolated using the direct plating inoculation method and then grown for a period of 7 days on a potato dextrose agar (PDA) with temperature set at 28 oC. The DNA was extracted from pure cultures and PCR was performed using primer in pair: ITS4 and ITS5. The products got from the PCR were sequenced for identification of species on the National Centre for Biotechnology Information (NCBI) database. Phylogenetic tree was generated based on the ITS1-2 gene sequences of the isolates. The 18 M. phaseolina isolates adopted for use in this study were all obtained from apparently healthy seeds of different varieties of groundnut sourced from local markets in Delta and Edo States, Nigeria. The experiment on germination of groundnut seeds was set up in a completely randomized design in ten replicates. The individual M. phaseolina isolates inhibited germination and seedling growth in varying degrees. The virulence of the isolates ranged from moderately pathogenic (50%) to extremely pathogenic (75%). Out of the 18 isolates, 14 were found to cause 100% mortality. The inoculated plants exhibited the disease symptoms (damping off, root rot, collar rot, necrosis, wilting and chlorosis) while the control remained healthy. Seedling emergence, number of leaves, root length, and stem girth of infected plants decreased when compared to the control.

Unearthing New ccr Genes and Staphylococcal Cassette Chromosome Elements in Staphylococci Through Genome Mining.

Staphylococcal cassette chromosome mec (SCCmec) typing is crucial for investigating methicillin-resistant Staphylococcus aureus (MRSA), relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB, and 3 ccrC) through mining of the National Center for Biotechnology Information (NCBI) database, forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of 5 groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.

Developing a comprehensive cell-free DNA (cfDNA) epigenetic signature (ep-Sig) with diagnostic and prognostic value in hepatocellular carcinoma (HCC).

553 Background: HCC is one of the deadliest tumors with poor outcomes often diagnosed in late stages. Current surveillance strategies (alfa-fetoprotein (AFP) plus ultrasound (USG)) for high-risk population (HRP) have poor sensitivity (SN) and reasonable specificity (SP) of 61% and 92%, respectively. Triple phase computed tomography (CT) imaging has good sensitivity and specificity (≈ 90% for both) but the evidence does not support its use for routine surveillance. All these modalities do not have prognostic (survival) value. We attempted to develop a non-invasive, cfDNA-based tests to improve the diagnostic value of the current standard of care modalities (AFP and USG) and help in predicting the outcomes at diagnosis. We hypothesized that RNA and gene expression in HCC tissues is a surrogate for epigenome (DNA-methylation changes). Methods: We curated a 21-gene cfDNA ep-Sig from the literature with a proven prognostic value. Evidence suggests epigenetic changes in every gene of this panel affect HCC outcomes influencing clinicopathological characteristics (large tumor size, vascular invasion, advanced staging) or early post-operative recurrence, and survival. We compared RNA and gene expression of the genes in the ep-Sig between normal (NT) and HCC tissues using a web-based tool, TNMplot.com that uses the data from the Gene Expression Omnibus of the National Center for Biotechnology Information (NCBI-GEO) or Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and The Genotype-Tissue Expression (GTEx) repositories was used create this tool. It uses Mann-Whitney or Kruskal-Wallis tests to compute statistical significance. Results: RNA expression of all the genes from the ep-Sig was significantly higher in HCC than NT (1.133, p=5.84e-15). Gene expression was 19/21 genes was higher in HCC tissues (1.15, p=1.3e-08). The other 2 genes were not detected in the tested samples. Conclusions: Our ep-Sig which has a proven prognostic value and reliable prevalence in HCC patients. This study is the first step in developing clinically useful blood-based test that can revamp the current diagnostic and screening practices when used alongside AFP and USG.

Developing cell-free DNA (cfDNA) epigenetic signature (ep-Sig) for early detection of malignant transformation of intraductal papillary mucinous neoplasms (IPMN).

616 Background: Pancreatic ductal adenocarcinoma (PDA) is one of the deadliest cancers with poor outcomes. Around 20% arise from premalignant lesions (PML) including IPMN. Current guidelines recommend risk stratifying IPMN based on the location, size, and imaging characteristics after first diagnosis, followed by endoscopic ultrasound (EUS) in high-risk populations, and annual or bi-annual imaging. This approach can be improved with cfDNA testing. Traditional mutation testing in cfDNA is not useful secondary to their poor prevalence/detection rates. We propose ep-Sig to improve surveillance and early detection of PDA transformation. Methods: We curated an 11-gene cfDNA ep-Sig from the literature with a proven role in the malignant transformation of IPMN. Evidence suggests that epigenetic changes in every gene of this panel have a role in carcinogenesis in IPMNs. We compared RNA and gene expression of the genes in this ep-Sig between normal (NT) and PDA tissues using a web-based tool, TNMplot.com that uses the data from the Gene Expression Omnibus of the National Center for Biotechnology Information (NCBI-GEO) or Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and The Genotype-Tissue Expression (GTEx) repositories was used create this tool. It uses Mann-Whitney or Kruskal-Wallis tests to compute statistical significance. We used cell-free epigenome atlas (CFEA) database to examine the prevalence of these markers in cfDNA of PDA patients. Results: RNA expression of all the genes from the ep-Sig combined was significantly lower in PDA than NT (0.45, p=3.13e-26). Gene expression was 8/11 genes was lower in PDA tissues than NT (0.44, p=3.13e-26). The other 2 genes were not detected in the tested samples. Prevalence of all the markers in ep-Sig was > 90%. Conclusions: Our proposed ep-Sig has a high prevalence in PDA patients and has reliable preliminary evidence in tissues suggesting its diagnostic value. This study is the first step in developing non-invasive cfDNA testing with the potential to improve the current surveillance strategies for IPMN pending larger prospective studies.

Finding Candida auris in public metagenomic repositories.

Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing.

Exploring a GtfB-Type 4,6-α-Glucanotransferase to Synthesize the (α1 → 6) Linkages in Linear Chain and Branching Points from Amylose and Enhance the Functional Property of Granular Corn Starches.

Starch-converting α-glucanotransferases of glycoside hydrolase family 70 (GH70) are promising enzymatic tools for the production of diverse α-glucans with (potential) commercial applications in food and health and as biomaterials. In this study, a novel GtfB enzyme from Weissella confusa MBF8-1 was screened in the National Center for Biotechnology Information (NCBI) nonredundant protein database. The enzyme (named WcMBF8-1 GtfB) displayed high conservation in motifs I-IV with other GtfB enzymes but possessed unique variations in several substrate-binding residues. Structural characterizations of its α-glucan products revealed that WcMBF8-1 GtfB exhibited an atypical 4,6-α-glucanotransferase activity and was capable of catalyzing, by cleaving off (α1 → 4)-linkages in starch-like substrates and the synthesis of linear (α1 → 6) linkages and (α1 → 4,6) branching points. The product specificity enlarges the diversity of α-glucans and facilitates recognition of the determinants of the linkage specificity in GtfB enzymes. Furthermore, the contents of slowly digestible starch and resistant starch of granular corn starches, modified by WcMBF8-1 GtfB, increased by 6.7%, which suggested the potential value for the utilization of WcMBF8-1 GtfB to prepare "clean-label" starch ingredients with improved functional attributes.

Analysis of gene characteristics and core genome characteristics of carbapenem-resistant Enterobacter cloacae in rural residents of Weifang City, Shandong Province

Objective: To investigate the drug-resistant gene characteristics and core genome characteristics of carbapenem-resistant Enterobacter cloacae (CR-ECL) in rural residents of Weifang City, Shandong Province. Methods: Fecal samples were collected from rural community residents in Weifang City, Shandong Province in 2017. Drug-resistant strains were screened using a carbapenem-resistant enterobacter chromogenic medium. CR-ECL positive strains were acquired via Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry(MALDI-TOFMS) analysis. The antibiotic resistance phenotype of CR-ECL was determined using a microbroth dilution assay. Whole genome sequencing (WGS) and analysis were conducted, along with an examination of the immediate vicinity of the blaNDM gene and phylogenetic analysis of the strains. Results: A total of 628 fecal samples were collected and tested, of which 6 were CR-ECL positive (detection rate 0.96%), all exhibiting multiple drug resistance (MDR) phenotypes. Six CR-ECL strains had four MLST genotypes (ST), all of which carried multiple drug resistance genes (blaNDM-1, blaNDM-5, etc.) and virulence genes (acrA, acrB, entB, fepC, etc.). There were mobile genetic elements ISAba125, TN3-IS3000, TN3 and IS5 in the genetic environment surrounding the blaNDM gene. The phylogenetic tree showed that the multi-locus sequence typing of the core genome (cgMLST) was consistent with the single nucleotide polymorphism (SNPs) results. The cgMLST results showed that the allele differences between strains 2BC0101B and 2BC0251B, 2BG0561B and 2BI0221B were 2 and 1, respectively. The SNPs results showed that the above two pairs of bacteria also clustered together. It was found that the strains of chicken fecal samples in the National Center for Biotechnology Information (NCBI) database were located in the center of the evolutionary tree, and the local sequences could be traced back to American human sequences. Conclusion: Multidrug-resistant CR-ECL is detected in rural community residents in Weifang City, Shandong Province.

Determination of Deleterious SNPs in NUDT15 Gene Related to Acute Lymphoblastic Leukemia by using Bioinformatics Tools

Aim: In acute lymphoblastic leukemia (ALL), thiopurine group drugs are the most basic drugs and are included in almost all treatment protocols, especially in maintenance treatment. The mechanism of action of thioguanine nucleotides is to enter the DNA structure in cells, disrupt DNA synthesis, and trigger programmed cell death. The impact of deleterious SNPs on nucleotide triphosphate diphosphatase protein regarding ALL is not yet fully understood. In this study, it was aimed to determine the possible deleterious impacts of missense variants in the NUDT15 gene on protein structure and stabilization that play a significant role in susceptibility to the disease, using modern bioinformatics software. Method: To access SNPs in the NUDT15, it was used National Center for Biotechnology Information (NCBI), Single Nucleotide Polymorphism Database (dbSNP). In bioinformatics tools used in this study included SIFT, PolyPhen-2, PROVEAN, SNAP2, and PANTHER, followed by I-Mutant, HOPE, and STRING. Results: The results of the analysis showed that in a total of 6663 SNPs in the NUDT15, 6 variants have been identified as ‘deleterious’. According to the I-Mutant software, 4 deleterious SNPs decreased protein stability while 2 deleterious SNPs increased protein stability. In the HOPE database analysis, E115G, E57G, F52L, and K33N mutant amino acids were found to be smaller and more hydrophobic than wild-type amino acids, while G53R and G145D mutant amino acids were found to be larger. Thus, all variations resulted in alterations in the net charge on the NUDT15 protein. Conclusion: Data on NUDT15 variants will contribute to the prediction of the patient’s response to thiopurine drugs in future studies, to a better understanding of the patient’s susceptibility to drug interactions, and ultimately to obtaining information about the prognosis.

Comparison of Metabarcoding Techniques for Dietary Assessment in Herbivores and Omnivores

Dietary assessment plays a crucial role in comprehending the ecological dynamics and nutritional needs of herbivores and omnivores. The metabarcoding technique has emerged as a potent tool for exploring the dietary composition of these animals. However, various metabarcoding techniques have been developed, each with its own advantages and limitations. This study aims to compare the performance of different metabarcoding techniques in herbivores and omnivores diet. We systematically reviewed 159 published manuscripts in Scopus and Google Scholar, and thematic analysis was conducted across several categories, including the marker, platform, and database utilized. Preliminary findings reveal significant variations among metabarcoding techniques across these two animal groups. The trnL gene exhibited higher taxonomic resolution for herbivorous species, whereas the combination of the 'trnL + 16s rRNA' gene exhibited superior performance for omnivorous species. The Illumina platform emerged as the most commonly used method for analyzing the diets of both herbivores and omnivores, with the primary reference database being the National Centre for Biotechnology Information (NCBI). This study offers valuable insights into the strengths and limitations of different metabarcoding techniques for dietary assessment in herbivores and omnivores and optimizing metabarcoding protocols, facilitating more precise and reliable diet analyses within these ecological groups.

First molecular phylogeny of Bartonella bovis in Iraqi cattle

Background: Bartonella bovis is one of the most neglected fastidious intracellular bacterial pathogens which infect a wide range of wild and domestic animals, including cattle. Aim: Detection of the prevalence of B. bovis in cattle using molecular assay, identification of the relationship of infection to animal risk factors (age and sex), and sequencing of B. bovis isolates to be analysed phylogenetically and reported in the National Centre For Biotechnology Information (NCBI). Methods: A total of 290 cattle were selected randomly from different rural areas in Wasit province during September to December (2023), and subjected to collecting venous blood samples that were tested molecularly by the polymerase chain reaction (PCR). Phylogenetic analysis was conducted using the MEGA 7 Software. Results: Targeting the 16S rRNA gene, 7.24% of the study cattle tested positive for B. bovis. In terms of age, positivity rates, Odds Ratios (OR), and Relative Risks (RR) were significantly higher in cattle older than 7 years compared to other age groups: under 1 year, 1-3 years, and 3-7 years. Regarding sex, there was no significant variation in positive rates between females (7.48%) and males (5.56%); however, the OR and RR values indicated that females (1.376 and 1.345, respectively) were at a higher risk of B. bovis infection than males (0.727 and 0.743, respectively). Phylogenetic tree analysis of five local B. bovis isolates demonstrated their identity with the France strain/isolate at total genetic identity ranging from 99.64-99.98%. Conclusion: To our knowledge, this study represents the first molecular identification of the prevalence rate of B. bovis in cattle in Iraq using PCR assay and confirms phylogenetically the local B. bovis isolates in NCBI-BLAST. Therefore, additional information about the prevalence, genetic diversity in domestic and wild animals, and arthropod vectors is crucial for developing strategies for the prevention and control of B. bovis infections.

Design and implementation of a TaqMan® real-time PCR method for detection and quantification of bovine leukemia virus.

The bovine leukemia virus (BLV) is an important infectious agent transmitted from cattle to humans. It is considered one of the oncogenic viruses in breast cancer, so an accurate detection of this virus is important. The study aimed to design a specific and sensitive method based on TaqMan® real-time polymerase chain reaction (RT-PCR) for BLV detection. Probes and primers were designed using bioinformatics software for a 108 pairs region of the BLV tax gene. Criteria employed for determining analytical sensitivity were prepared using in-vitro RNA transcriptions. The National Center for Biotechnology Information (NCBI), basic local alignment search tool (BLAST) databases various viral panels and genomic samples from healthy individuals (Qom Province, Iran in 2023) were used to verify analytical specificity and clinical specificity, respectively. This method can measure a minimum of 10 copies of DNA and RNA mL-1. Moreover, the assay is linear in the range of 100 - 109 copies mL-1. By testing negative specimens, the method specificity was 100%. The reproducibility results of the reaction were examined at the intra- and inter-assay comparison. In fact, 10 technical replicates of each concentration of the control sample were analyzed in each working reaction. Due to the locally made kit, exact sensitivity and specificity, rapid analysis, and relatively low cost, as compared to commercial kits of other countries, the method introduced in the present study could be suitable for accurate detection of the BLV. Also, the TaqMan® real-time PCR method could be detected in cattle and human and before malignant changes of breast cancer which could reduce infection and breast cancer.

Comparative Transcriptomics Data Profiling Reveals E2F Targets as an Important Biological Pathway Overexpressed in Intellectual Disability Disorder.

Intellectual disability (ID) is an early childhood neurodevelopmental disorder that is characterized by impaired intellectual functioning and adaptive behavior. It is one of the major concerns in the field of neurodevelopmental disorders across the globe. Diversified approaches have been put forward to overcome this problem. Among all these approaches, high throughput transcriptomic analysis has taken an important dimension. The identification of genes causing ID rapidly increased over the past 3 to 5 years owing to the use of sophisticated high throughput sequencing platforms. Early monitoring and preventions are much important for such disorder as their progression occurs during fetal development. This study is an attempt to identify differentially expressed genes (DEGs) and upregulated biological processes involved in development of ID patients through comparative analysis of available transcriptomics data. A total of 7 transcriptomic studies were retrieved from National Center for Biotechnology Information (NCBI) and were subjected to quality check and trimming prior to alignment. The normalization and differential expression analysis were carried out using DESeq2 and EdgeR packages of Rstudio to identify DEGs in ID. In progression of the study, functional enrichment analysis of the results obtained from both DESeq2 and EdgeR was done using gene set enrichment analysis (GSEA) tool to identify major upregulated biological processes involved in ID. Our findings concluded that monitoring the level of E2F targets, estrogen, and genes related to oxidative phosphorylation, DNA repair, and glycolysis during the developmental stage of an individual can help in the early detection of ID disorder.

Molecular Identification of Fusarium Species Associated with the Tissue Culture Date Palm Offshoots Wilt Disease and Evaluation of Using Silver Nanoparticles and Trichoderma longibrachiatum for Its Control

Fayyadh, M.A., A.O. Manea and Y.A. Salih. 2024. Molecular Identification of Fusarium Species Associated with the Tissue Culture Date Palm Offshoots Wilt Disease and Evaluation of Using Silver Nanoparticles and Trichoderma longibrachiatum for Its Control. Arab Journal of Plant Protection, 42(2): 189-195. https://doi.org/10.22268/AJPP-001225 This study was conducted during the period 2019-2021 with the aim of isolating and identifying the fungi associated with the tissue culture date palm offshoots wilt disease planted in permanent orchards. Molecular identification of Fusarium isolates based on amplification and nucleotide sequencing of the ITS1-ITS4 gene region showed that isolate F1 and F7 were identical to F. proliferatum with a similarity level of 100 and 98%, respectively; isolates F3 and F4 were identical to F. fujikuroi with a similarity level of 99.8 and 100%, respectively. As for isolate F6, it was 94.8% similar with F. solani. The sequences of the identified isolates were deposited in the US National Center for Biotechnology Information (NCBI) under the numbers OM535259.1, OM535261.1, OM535264.1, OM535265.1 and OM535266.1, respectively. The results also showed that silver nanoparticles inhibited the growth of all tested fungi, and the inhibition rate range was 50- 70%. On the other hand, the bio-control fungus T. longibrachiatum caused growth inhibition of all tested fungi with an inhibition rate of more than 80%. Keywords: Date palm, wilt, molecular identification, nanosiliver particles

First molecular sequencing of Babesia gibsoni in ticks, Iraq.

Tick is one of the most important ectoparasites distributed worldwide and plays an obvious role in the transmission of different infections to humans and animals as dogs. This study conducted to molecular demonstration of Babesia gibsoni in ticks of stray dogs and phylogenetic analysis of study isolates to detect their identity to global isolates. Prevalence of ticks in dogs, identification of tick species, and their relationship to some risk factors were aimed, also. A total of 97 stray dogs were inspected grossly to detect and collect ticks that existed in different body parts. After collection, all ticks were examined morphologically to identify their species, and then molecularly by the polymerase chain reaction (PCR) assay to detect B. gibsoni in different species of ticks. Local B. gibsoni isolates were sequenced, documented in the National Center For biotechnology information (NCBI) database, analyzed phylogenetically, and compared with the global GenBank-NCBI isolates. In the current study, ticks were detected in 43.3% of dogs, and were shown to be varied in number and distribution among different body parts of each dog. Concerning its distribution, ticks were observed significantly on the abdomen, ear, and perineal region. In relation to risk factors, ticks were increased significantly in dogs <6 months old in comparison to older dogs, males more than females; and in rural areas more than dogs of sub-urban and urban areas. Based on morphology, different tick species were seen including Hylaomma anatolicum (86.12%), R. sanguineus (11.99%), and Rhipicephalus turanicus (1.89%). Targeting the 18S rRNA gene, PCR assay reported 3.79% positive ticks to B. gibsoni that were seen in R. sanguineus (13.16%) and H. anatolicum (2.56%). Based on phylogenetic analysis data of five local B. gibsoni isolates, this study demonstrated their close relations to the global NCBI-BLAST B. gibsoni Iraqi isolate (ID: MN385424.1). This represents the first Iraqi study that demonstrated molecularly B. gibsoni in different species of ticks that infected stray dogs.

A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus).

Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.

Integrated Multi-Omics Analysis and Validation in Yeast Model of Amyotrophic Lateral Sclerosis.

Transcriptomics is a complex process that involves raw data extraction, normalization, differential gene expression, and analysis. The Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) is a repository of experimental datasets. Amyotrophic lateral sclerosis (ALS) datasets are deposited by various scientists and research investigators to expand the horizon of scientific knowledge. R-statistical tools are the most common ways for conducting these kinds of studies. The first step is the identification of appropriate datasets. Since the raw data is available in a variety of formats, a large array of software is used for extraction and analysis. Normalization is conducted for the datasets using NetworkAnalyst. Differential analysis is further conducted on the normalized data to identify significantly enriched genes. The significant genes are then grouped into pathways. The results were validated using yeast model of ALS in which the yeast is transformed with ALS plasmids encoding genes associated with ALS. The resulting GFP-tagged protein aggregates are imaged using fluorescence microscopy and subsequently validated using filter retardation assay and quantified using ImageJ software. Functional role of different genes is studied using metabolite treatment and knockout studies.