Genomic Identification Research Articles

Correction for Hon et al., "Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore".

Correction for Hon et al., "Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore".

PlastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets

The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.

Emergence and Genomic Features of a mcr-1 Escherichia coli from Duck in Hungary.

Plasmids carrying high-risk resistance mechanisms in pathogenic E. coli have gained particular attention in veterinary medicine, especially since the discovery of the colistin resistance gene, mcr-1. Here, we provide the first evidence of its emergence and describe the complete mcr-1 plasmid sequence of a multi-resistant avian pathogenic E. coli (APEC) strain from waterfowl in Hungary. Whole-genome sequencing analysis and core-genome MLST were performed to characterize the genome structure of the mcr-1 plasmid and to reveal the phylogenetic relation between the Hungarian duck strain Ec45-2020 and the internationally circulating mcr-1-positive E. coli strains from poultry and humans. Results showed that plasmid pEc45-2020-33kb displayed a high level of genome identity with mcr-1 plasmids of IncX4 type widespread among human, animal and food reservoirs of enteric bacteria of public health. The mcr-1-positive E. coli strain Ec45-2020 belongs to the ST162 genotype, considered as one of the globally disseminated zoonotic genotypes of MDR E. coli. In accordance with international findings, our results underline the importance of continuous surveillance of enteric bacteria with high-risk antimicrobial resistance genotypes, including neglected animals, such as waterfowls, as possible reservoirs for the colistin resistance gene mcr-1.

Advancements in the Management of Endocrine System Disorders and Arrhythmias: A Comprehensive Narrative Review.

In recent years, notable advancements have been made in managing endocrine system disorders and arrhythmias. These advancements have brought about significant changes in healthcare providers' approach towards these complex medical conditions. Endocrine system disorders encompass a diverse range of conditions, including but not limited to diabetes mellitus, thyroid dysfunction, and adrenal disorders. Significant advancements in comprehending the molecular underpinnings of these disorders have laid the foundation for implementing personalized medicine. Advancements in genomic profiling and biomarker identification have facilitated achieving more accurate diagnoses and developing customized treatment plans. Furthermore, the utilization of cutting-edge pharmaceuticals and advanced delivery systems presents a significant advancement in achieving enhanced glycemic control and minimizing adverse effects for individuals afflicted with endocrine disorders. Arrhythmias, characterized by irregular heart rhythms, present a substantial risk to cardiovascular well-being. Innovative strategies for managing arrhythmia encompass catheter-based ablation techniques, wearable cardiac monitoring devices, and predictive algorithms powered by artificial intelligence. These advancements facilitate the early detection, stratification of risks, and implementation of targeted interventions, ultimately leading to improved patient outcomes. Incorporating technology and telemedicine has been instrumental in enhancing the accessibility and continuity of care for individuals diagnosed with endocrine disorders and arrhythmias. The utilization of remote patient monitoring and telehealth consultations enables prompt modifications to treatment regimens and alleviates the need for frequent visits to the clinic. This is particularly significant in light of the current global health crisis. This review highlights the interdisciplinary nature of managing endocrine disorders and arrhythmias, underscoring the significance of collaboration among endocrinologists, cardiologists, electrophysiologists, and other healthcare professionals. Multidisciplinary care teams have enhanced their capabilities to effectively address the intricate relationship between the endocrine and cardiovascular systems. In summary, endocrine system disorders and arrhythmias management have undergone significant advancements due to groundbreaking research, technological advancements, and collaborative healthcare approaches. This narrative review provides a comprehensive overview of the advancements, showcasing their potential to enhance patient care, improve quality of life, and decrease healthcare expenses. Healthcare providers must comprehend and integrate these advancements into their clinical practice to enhance outcomes for individuals with endocrine system disorders and arrhythmias.

Evaluation of Fourier transform-infrared spectroscopy (FT-IR) as a control measure for nosocomial outbreak investigations.

Whole-genome sequencing (WGS) provides greater resolution than other molecular epidemiology strategies and is emerging as a new gold standard approach for microbial strain typing. The Bruker IR Biotyper is designed as a screening tool to identify bacterial isolates that require WGS to establish accurate relationships, but its performance and utility in nosocomial outbreak investigations have not been thoroughly investigated. Here, we evaluated the IR Biotyper by retrospectively examining isolates tested by WGS during investigations of potential nosocomial transmission events or outbreaks. Ninety-eight clinical isolates from 14 different outbreak investigations were examined: three collections of Acinetobacter baumannii (n = 2, n = 9, n = 5 isolates in each collection), one of Escherichia coli (n = 16), two of Pseudomonas aeruginosa (n = 2 and n = 5), two of Serratia marcescens (n = 9 and n = 7), five of Staphylococcus aureus (n = 8, n = 4, n = 3, n = 3, n = 17), and one of Stenotrophomonas maltophilia (n = 8). Linear regression demonstrated a weak, positive correlation between the number of pairwise genome-wide single-nucleotide polymorphisms (SNPs) and IR Biotyper spectral distance values for Gram-positive (r = 0.43, P ≤ 0.0001), Gram-negative (r = 0.1554, P = 0.0639), and all organisms combined (r = 0.342, P ≤ 0.0001). Overall, the IR Biotyper had a positive predictive value (PPV) of 55.81% for identifying strains that were closely related by genomic identity, but a negative predictive value (NPV) of 86.79% for identifying unrelated isolates. When experimentally adjusted cut-offs were applied to A. baumannii, P. aeruginosa, and E. coli, the PPV was 62% for identifying strains that were closely related and the NPV was 100% for identifying unrelated isolates. Implementation of the IR Biotyper as a screening tool in this cohort would have reduced the number of Gram-negative isolates requiring further WGS analysis by 50% and would reduce the number of S. aureus isolates needing WGS resolution by 48%.

S156 New, Under-Recognized Genomic Alterations Enable Early Identification of High-Risk Pancreatic Cysts Likely to Progress to Malignancy

S156 New, Under-Recognized Genomic Alterations Enable Early Identification of High-Risk Pancreatic Cysts Likely to Progress to Malignancy

MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes.

A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.

Molecular investigations of camelpox virus circulating in dromedary camel population in Rajasthan, India

Camelpox is an important viral disease of dromedary camel in Rajasthan, India. In the present study, partial C18L gene sequences (n = 6) of camelpox virus (CMLV) obtained in an outbreak in Bikaner, Rajasthan, India in year 2022 were compared with other similar sequences obtained in the past in similar geographical location. Clinical and epidemiological features of the disease were also compared. Genomic study suggested variations in C18L gene sequences obtained in the present outbreak from those obtained during the past outbreaks. CMLV were genetically different from cowpox viruses, but appeared identical to CMLV causing disease in Israel, Egypt and Kazakhstan. Genomes of CMLV virus circulating in dromedary camel population of Rajasthan, India appeared diverse and changing, hence complete genome sequencing and identification of genomic changes altering infectivity and pathogenicity is warranted for designing control strategies.

DEEPENED GENOMICS-METABOLOMICS CHARACTERISTICS OF THE BACTERIA OF THE BACILLUS GENUS ISOLATED FROM DEEP-SEA

Marine bacteria from the genus Bacillus are attracting increasing attention as a source of large amounts of bioactive metabolites. The biosynthetic potential of marine bacteria from the genus Bacillus is not sufficiently studied. The previous study of authors could not give a complete result, so it was decided to reanalyze the metabolites not identified at that time, taking into account the development of existing databases. Therefore, the work aimed to reanalyze the metabolome already performed on Bacillus velezensis ONU 553, Bacillus pumilus ONU 554, and Bacillus subtilis ONU 559 strains isolated from the Black Sea sediments. Methods. The general genome identification was performed using the online version of the Dictionary of Natural Products database, and search for biosynthetic clusters in genome of Bacillus velezensis ONU 553 - with antiSMASH 7.0. Results and Conclusion. Genomic-metabolic profiling of strains led to the identification of several new biological compounds – 7 and 1 metabolites in Bacillus velezensis ONU 553 and Bacillus pumilus ONU 554 strains, respectively, and to identify biosynthetic clusters of iturin- and helipeptin-like peptides in Bacillus velezensis ONU 553 strain for the first time. A new biosynthetic cluster was found in the Bacillus velezensis ONU 553 strain.

Genomic Identification and Expression Profiling of Lesion Simulating Disease Genes in Alfalfa (Medicago sativa) Elucidate Their Responsiveness to Seed Vigor.

Seed aging, a common physiological phenomenon during forage seed storage, is a crucial factor contributing to a loss of vigor, resulting in delayed seed germination and seedling growth, as well as limiting the production of hay. Extensive bodies of research are dedicated to the study of seed aging, with a particular focus on the role of the production and accumulation of reactive oxygen species (ROS) and the ensuing oxidative damage during storage as a primary cause of decreases in seed vigor. To preserve optimal seed vigor, ROS levels must be regulated. The excessive accumulation of ROS can trigger programmed cell death (PCD), which causes the seed to lose vigor permanently. LESION SIMULATING DISEASE (LSD) is one of the proteins that regulate PCD, encodes a small C2C2 zinc finger protein, and plays a molecular function as a transcriptional regulator and scaffold protein. However, genome-wide analysis of LSD genes has not been performed for alfalfa (Medicago sativa), as one of the most important crop species, and, presently, the molecular regulation mechanism of seed aging is not clear enough. Numerous studies have also been unable to explain the essence of seed aging for LSD gene regulating PCD and affecting seed vigor. In this study, we obtained six MsLSD genes in total from the alfalfa (cultivar Zhongmu No. 1) genome. Phylogenetic analysis demonstrated that the MsLSD genes could be classified into three subgroups. In addition, six MsLSD genes were unevenly mapped on three chromosomes in alfalfa. Gene duplication analysis demonstrated that segmental duplication was the key driving force for the expansion of this gene family during evolution. Expression analysis of six MsLSD genes in various tissues and germinating seeds presented their different expressions. RT-qPCR analysis revealed that the expression of three MsLSD genes, including MsLSD2, MsLSD5, and MsLSD6, was significantly induced by seed aging treatment, suggesting that they might play an important role in maintaining seed vigor. Although this finding will provide valuable insights into unveiling the molecular mechanism involved in losing vigor and new strategies to improve alfalfa seed germinability, additional research must comprehensively elucidate the precise pathways through which the MsLSD genes regulate seed vigor.

Molecular characterization of MRSA collected during national surveillance between 2008 and 2019 in the Netherlands

Background.Although the Netherlands is a country with a low endemic level, methicillin-resistant Staphylococcus aureus (MRSA) poses a significant health care problem. Therefore, high coverage national MRSA surveillance has been in place since 1989. To monitor possible changes in the type-distribution and emergence of resistance and virulence, MRSA isolates are molecularly characterized.Methods.All 43,321 isolates from 36,520 persons, collected 2008–2019, were typed by multiple-locus variable number tandem repeats analysis (MLVA) with simultaneous PCR detection of the mecA, mecC and lukF-PV genes, indicative for PVL. Next-generation sequencing data of 4991 isolates from 4798 persons were used for whole genome multi-locus sequence typing (wgMLST) and identification of resistance and virulence genes.Results.We show temporal change in the molecular characteristics of the MRSA population with the proportion of PVL-positive isolates increasing from 15% in 2008–2010 to 25% in 2017–2019. In livestock-associated MRSA obtained from humans, PVL-positivity increases to 6% in 2017–2019 with isolates predominantly from regions with few pig farms. wgMLST reveals the presence of 35 genogroups with distinct resistance, virulence gene profiles and specimen origin. Typing shows prolonged persistent MRSA carriage with a mean carriage period of 407 days. There is a clear spatial and a weak temporal relationship between isolates that clustered in wgMLST, indicative for regional spread of MRSA strains.Conclusions.Using molecular characterization, this exceptionally large study shows genomic changes in the MRSA population at the national level. It reveals waxing and waning of types and genogroups and an increasing proportion of PVL-positive MRSA.

Characterization of three rapidly growing novel Mycobacterium species with significant polycyclic aromatic hydrocarbon bioremediation potential.

Mycobacterium species exhibit high bioremediation potential for the degradation of polycyclic aromatic hydrocarbons (PAHs) that are significant environmental pollutants. In this study, three Gram-positive, rapidly growing strains (YC-RL4T, MB418T, and HX176T) were isolated from petroleum-contaminated soils and were classified as Mycobacterium within the family Mycobacteriaceae. Genomic average nucleotide identity (ANI; < 95%) and digital DNA-DNA hybridization (dDDH; < 70%) values relative to other Mycobacterium spp. indicated that the strains represented novel species. The morphological, physiological, and chemotaxonomic characteristics of the isolates also supported their affiliation with Mycobacterium and their delineation as novel species. The strains were identified as Mycobacterium adipatum sp. nov. (type strain YC-RL4T = CPCC 205684T = CGMCC 1.62027T), Mycobacterium deserti sp. nov. (type strain MB418T = CPCC 205710T = KCTC 49782T), and Mycobacterium hippophais sp. nov. (type strain HX176T = CPCC 205372T = KCTC 49413T). Genes encoding enzymes involved in PAH degradation and metal resistance were present in the genomes of all three strains. Specifically, genes encoding alpha subunits of aromatic ring-hydroxylating dioxygenases were encoded by the genomes. The genes were also identified as core genes in a pangenomic analysis of the three strains along with 70 phylogenetically related mycobacterial strains that were previously classified as Mycolicibacterium. Notably, strain YC-RL4T could not only utilize phthalates as their sole carbon source for growth, but also convert di-(2-ethylhexyl) phthalate into phthalic acid. These results indicated that strains YC-RL4T, MB418T, and HX176T were important resources with significant bioremediation potential in soils contaminated by PAHs and heavy metals.

Occurrence, Characteristics, and qPCR-Based Identification of Pectobacterium versatile Causing Soft Rot of Chinese Cabbage in China.

Pectobacterium is one of the most important genera of phytopathogenic bacteria. It can cause soft-rot diseases on a wide range of plant species across the world. In this study, three Pectobacterium strains (KC01, KC02, and KC03) were isolated from soft-rotted Chinese cabbage in Beijing, China. These three strains were identified as Pectobacterium versatile based on phylogenetic analysis of Pectobacterium 16S ribosomal RNA, pmrA, and 504 Pectobacterium core genes, as well as a genomic average nucleotide identity analysis. Their biochemical characteristics were found to be similar to the P. versatile type strain ICMP9168T but differed in response to citric acid, stachyose, D-glucuronic acid, dextrin, and N-acetyl-β-D-mannosamine. All of the tested P. versatile strains showed different carbohydrate utilization abilities compared with P. carotovorum and P. odoriferum, particularly in their ability to utilize D-arabitol, L-rhamnose, and L-serine. Under laboratory conditions, the maceration ability of P. versatile on Chinese cabbage was the highest at 28°C, compared with those at 13, 28, 23, and 33°C. Additionally, P. versatile could infect all of the 17 known Pectobacterium host plants, except for Welsh onion (Allium fistulosum). A SYBR Green quantitative PCR (qPCR) detection system was developed to distinguish P. versatile from other soft-rot bacteria based on the combined performance of melting curve (with a single melting peak at around 85°C) and fluorescence curve (with cycle threshold <30) when the bacterial genomic DNA concentration was in the range of 10 pg/µl to 10 ng/µl. This study is the first to report the presence of P. versatile on Chinese cabbage in China, as well as a specific and sensitive qPCR assay that can be used to quickly identify P. versatile. The work contributes to a better understanding of P. versatile and will facilitate the effective diagnosis of soft-rot disease, ultimately benefitting commercial crop production.

Genomic molecular epidemiology of carbapenemase-producing Escherichia coli ST410 isolates by complete genome analysis

The circulation of carbapenemase-producing Escherichia coli (CPEC) in our society is a serious concern for vulnerable patients in nosocomial environments. However, the genomic epidemiology of the circulation of CPEC bacteria among companion animals remains largely unknown. In this study, epidemiological analysis was conducted using complete genome identification of CPEC ST410 isolates obtained from companion animals. To estimate the genomic distance and relatedness of the isolates, a total of 37 whole-genome datasets of E. coli ST410 strains were downloaded and comparatively analysed. As a result of the analysis, the genomic structure of the chromosomes and plasmids was identified, revealing the genomic positions of multiple resistance and virulence genes. The isolates in this study were grouped into the subclade H24/RxC, with fimH24, and substituted quinolone resistance-determining regions (QRDRs) and multiple beta-lactamases, including extended-spectrum β-lactamase (ESBL) and carbapenemase. In addition, the in silico comparison of the whole-genome datasets revealed unidentified ST410 H24/Rx subgroups, including either high pathogenicity islands (HPIs) or H21 serotypes. Considering the genetic variations and resistance gene dissemination of the isolates carried by companion animals, future approaches for preventive measurement must include the “One Health” perspective for public health in our society.

Modern Approaches to Criminalistic Identification: The Role of Genomic Identification

Criminalistic identification is an important instrument in the investigation of crimes. The article analyzes the classification of identification methods with an emphasis on genomic identification. The importance of applying modern methods of genomic identification in criminalistics is stressed, the problems associated with the collection of specimens for comparative research are studied, and the requirements to the collection of traces of biological origin are described. The author presents a review of publications and current research methods in the field of criminalistic identification. A classification of criminalistic identification based on different criteria is given, including the criteria of legal nature, type of reflection, evidential significance and properties of identified objects. Key methods of genomic identification, such as the polymerase chain reaction (PCR), microsatellite analysis, DNA sequencing and others are examined within the context of their application in criminalistics. The author presents the results of analyzing the existing methods of genomic identification and the problems connected with specimen collection. The requirements to the collection of traces of biological origin are identified. However, it is considered impossible to offer a universal algorithm of identifying, collecting and preserving biological evidence. The analysis of the results allows the author to draw conclusions about the importance of genomic identification in criminalistics and the necessity of observing requirements to collecting the traces of biological origin.

Limited hybridisation and introgression despite stocking among endemic Interior Highlands black basses (Centrarchidae: Micropterus)

AbstractAimSmallmouth Bass (Micropterus dolomieu; SMB) are globally popular among anglers and have been widely introduced (i.e. stocked) for population management and sportfishing. Importantly, stocking was prevalent before cryptic diversity within the SMB complex was known, which now includes three newly elevated species: Neosho Bass (M. velox; NB), Little River Bass (M. sp. cf. dolomieu Little River; LRB) and Ouachita Bass (M. sp. cf. dolomieu Ouachita River; OB). We sought to quantify population structure and hybridisation and introgression in these three recently described species.LocationSpecies‐level diversity, particularly in the basin‐restricted LRB and OB in the Ouachita Mountains within the Central Interior Highlands (CIH), North America, suggests the presence of distinct genetic variation that could be eroded by introgression.MethodsWe estimated interspecific introgression and intraspecific population differentiation in the Smallmouth Bass species complex (SMB‐C) using 472 specimens comprising SMB, NB, LRB and OB, including the naturally sympatric Spotted Bass (M. punctulatus; SPB). Genomic samples were genotyped on a SNP panel of 192 loci designed to detect allele‐sharing on multiple hierarchical levels.ResultsWe found low range‐wide hybridisation between species in the SMB‐C and SPB (mostly SMB‐C backcrosses), and interspecific heterozygosity varied, indicating differential introgression. Range‐wide hybridisation between species in the CIH and SMB was similar overall (but mostly F2 and CIH backcrosses) and was observed in streams with known SMB stocking in connected reservoirs. Interspecific heterozygosity in SMB hybrids was also generally lower, indicating later‐generation backcrosses. We found strong population structure in the Ouachita Mountains (LRB and OB).Main ConclusionsDespite isolated incidences of natural (SPB) and human‐mediated (SMB) introgression, genomic identity appears intact in endemic LRB and OB, suggesting potential ecological or behavioural isolating mechanisms preventing cross‐species reproduction. Our findings reveal that genetic variation remains in cryptic, basin‐restricted species in the Ouachita Mountains ecoregion that may be managed for long‐term conservation.

Gillisia lutea sp. nov., isolated from marine aluminium residues from the Mediterranean sea.

A novel Gram-reaction-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore forming, orange-pigmented bacterium identified as M10.2AT, was isolated from marine residues submerged on the Malva-rosa beach (València, Spain), on the western coast of the Mediterranean Sea. This strain was catalase-positive and oxidase-negative and grew under mesophilic, neutrophilic and halophilic conditions. With respect to the 16S rRNA gene sequences, M10.2AT showed similarities with Gillisia mitskevichiae DSM 19839T and Gillisia hiemivida IC154T (97.57 and 97.50 % gene sequence similarity, respectively). The genome of M10.2AT was sequenced and has been deposited in the DDBJ/ENA/GenBank databases under the accession code JAKGTH000000000. The genomic DNA G+C content was 36.13 %. Its adscription to a novel species of the genus Gillisia was confirmed by the genomic indexes average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridisation (dDDH). The major fatty acids were iso-C15 : 0, iso-C15 : 1G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to the results of this polyphasic study, strain M10.2AT represents a novel species of the genus Gillisia, for which name Gillisia lutea sp. nov. (type strain M10.2AT = CECT 30308T = DSM 112385T) is proposed.

Genome Identification and Evolutionary Analysis of LBD Genes and Response to Environmental Factors in Phoebe bournei.

Phoebe bournei is nationally conserved in China due to its high economic value and positive effect on the ecological environment. P. bournei has an excellent wood structure, making it useful for industrial and domestic applications. Despite its importance, there are only a few studies on the lateral organ boundary domain (LBD) genes in P. bournei. The LBD gene family contributes to prompting rooting in multiple plant species and therefore supports their survival directly. To understand the LBD family in P. bournei, we verified its characteristics in this article. By comparing the sequences of Arabidopsis and identifying conserved domains and motifs, we found that there were 38 members of the LBD family in P. bournei, which were named PbLBD1 to PbLBD38. Through evolutionary analysis, we found that they were divided into two different populations and five subfamilies in total. The LBD gene family in P. bournei (Hemsl.) Yang species had two subfamilies, including 32 genes in Class I and 6 genes in Class II. It mainly consists of a Lateral Organ Boundary (LOB) conservative domain, and the protein structure is mostly "Y"-shaped. The gene expression pattern of the LBD gene family showed that the LBD genes were mainly expressed in lateral organs of plants, such as flowers and fruits. The response of LBD transcription factors to red and blue light was summarized, and several models of optogenetic expression regulation were proposed. The effect of regulatory mechanisms on plant rooting was also predicted. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PbLBDs were differentially expressed under cold, heat, drought, and salt stresses, indicating that PbLBDs might play different functions depending on the type of abiotic stress. This study provides the foundation for further research on the function of LBD in this tree species in the future.

Characterization and genomics identification of key genes involved in denitrification-DNRA-nitrification pathway of plant growth-promoting rhizobacteria (Serratia marcescens OK482790)

BackgroundA wide variety of microorganisms, including bacteria, live in the rhizosphere zone of plants and have an impact on plant development both favorably and adversely. The beneficial outcome is due to the presence of rhizobacteria that promote plant growth (PGPR).ResultsIn this study, a bacterial strain was isolated from lupin rhizosphere and identified genetically as Serratia marcescens (OK482790). Several biochemically and genetically characteristics were confirmed in vitro and in vivo to determine the OK482790 strain ability to be PGPR. The in vitro results revealed production of different lytic enzymes (protease, lipase, cellulase, and catalase), antimicrobial compounds (hydrogen cyanide, and siderophores), ammonia, nitrite, and nitrate and its ability to reduce nitrate to nitrite. In silico and in vitro screening proposed possible denitrification-DNRA-nitrification pathway for OK482790 strain. The genome screening indicated the presence of nitrite and nitrate genes encoding Nar membrane bound sensor proteins (NarK, NarQ and NarX). Nitrate and nitrite reductase encoding genes (NarI, NarJ, NarH, NarG and NapC/NirT) and (NirB, NirC, and NirD) are also found in addition to nitroreductases (NTR) and several oxidoreductases. In vivo results on wheat seedlings confirmed that seedlings growth was significantly improved by soil inoculation of OK482790 strain.ConclusionsThis study provides evidence for participation of S. marcescens OK482790 in nitrogen cycling via the denitrification-DNRA-nitrification pathway and for its ability to produce several enzymes and compounds that support the beneficial role of plant-microbe interactions to sustain plant growth and development for a safer environment.

Leveraging polymer modeling to reconstruct chromatin connectivity from live images

Chromosomal dynamics plays a central role in a number of critical biological processes, such as transcriptional regulation, genetic recombination, and DNA replication. However, visualization of chromatin is generally limited to live imaging of a few fluorescently labeled chromosomal loci or high-resolution reconstruction of multiple loci from a single time frame. To aid in mapping the underlying chromosomal structure based on parsimonious experimental measurements, we present an exact analytical expression for the evolution of the polymer configuration based on a flexible-polymer model, and we propose an algorithm that tracks the polymer configuration from live images of chromatin marked with several fluorescent marks. Our theory identifies the resolution of microscopy needed to achieve high-accuracy tracking for a given spacing of markers, establishing the statistical confidence in the assignment of genome identity to the visualized marks. We then leverage experimental data of locus-tracking measurements to demonstrate the validity of our modeling approach and to establish a basis for the design of experiments with a desired resolution. Altogether, this work provides a computational approach founded on polymer physics that vastly improves the interpretation of in vivo measurements of biopolymer dynamics.