Pool Of Genes Research Articles

The Human Gut Resistome up to Extreme Longevity.

ABSTRACTAntibiotic resistance (AR) is indisputably a major health threat which has drawn much attention in recent years. In particular, the gut microbiome has been shown to act as a pool of AR genes, potentially available to be transferred to opportunistic pathogens. Herein, we investigated for the first time changes in the human gut resistome during aging, up to extreme longevity, by analyzing shotgun metagenomics data of fecal samples from a geographically defined cohort of 62 urban individuals, stratified into four age groups: young adults, elderly, centenarians, and semisupercentenarians, i.e., individuals aged up to 109 years. According to our findings, some AR genes are similarly represented in all subjects regardless of age, potentially forming part of the core resistome. Interestingly, aging was found to be associated with a higher burden of some AR genes, including especially proteobacterial genes encoding multidrug efflux pumps. Our results warn of possible health implications and pave the way for further investigations aimed at containing AR accumulation, with the ultimate goal of promoting healthy aging.IMPORTANCE Antibiotic resistance is widespread among different ecosystems, and in humans it plays a key role in shaping the composition of the gut microbiota, enhancing the ecological fitness of certain bacterial populations when exposed to antibiotics. A considerable component of the definition of healthy aging and longevity is associated with the structure of the gut microbiota, and, in this regard, the presence of antibiotic-resistant bacteria is critical to many pathologies that come about with aging. However, the structure of the resistome has not yet been sufficiently elucidated. Here, we show distinct antibiotic resistance assets and specific microbial consortia characterizing the human gut resistome through aging.

Genetic Analysis, Population Structure, and Characterisation of Multidrug-Resistant Klebsiella pneumoniae from the Al-Hofuf Region of Saudi Arabia.

Multidrug-resistant Klebsiella pneumoniae (MDR-KP) is a major public health problem that is globally associated with disease outbreaks and high mortality rates. As the world seeks solutions to such pathogens, global and regional surveillance is required. The aim of the present study was to examine the antimicrobial susceptibility pattern and clonal relatedness of Klebsiella pneumoniae isolates collected for a period of three years through pulse field gel electrophoresis (PFGE). Isolate IDs, antimicrobial assays, ESBL-production, and minimum inhibitory concentrations (MICs) were examined with the Vitek 2 Compact Automated System. IDs were confirmed by 16S rRNA gene sequencing, with the resulting sequences being deposited in NCBI databases. DNA was extracted and resistance genes were detected by PCR amplification with appropriate primers. Isolates were extensive (31%) and multidrug-resistant (65%). Pulsotype clusters grouped the isolates into 22 band profiles that showed no specific pattern with phenotypes. Of the isolates, 98% were ESBL-KP, 69% were carbapenem-resistant Enterobacteriaceae (CRE) strains, and 72.5% comprised the carriage of two MBLs (SIM and IMP). Integrons (ISAba1, ISAba2, and IS18) were detected in 69% of the MDR-KP. Additionally, OXA-23 was detected in 67% of the isolates. This study therefore demonstrates clonal diversity among clinical K. pneumoniae, confirming that this bacterium has access to an enormous pool of genes that confer high resistance-developing potential.

IRGvalid: A Robust in silico Method for Optimal Reference Gene Validation.

BackgroundAppropriate reference genes are critical to accurately quantifying relative gene expression in research and clinical applications. Numerous efforts have been made to select the most stable reference gene(s), but a consensus has yet to be achieved. In this report, we propose an in silico reference gene validation method, iRGvalid, that can be used as a universal tool to validate the reference genes recommended from different resources so as to identify the best ones without a need for any wet lab validation tests.MethodsiRGvalid takes advantage of high throughput gene expression data and is built on a double-normalization strategy. First, the expression level of each individual gene is normalized against the total gene expression level of each sample, followed by a target gene normalization to the candidate reference gene(s). Linear regression analysis is then performed between the pre- and post- normalized target gene across the whole sample set to evaluate the stability of the reference gene(s), which is positively associated with the Pearson correlation coefficient, Rt. The higher the Rt value, the more stable the reference gene. We applied iRGvalid to 14 candidate reference genes to validate and identify the most stable reference genes in four cancer types: lung adenocarcinoma, breast cancer, colon adenocarcinoma, and nasopharyngeal cancer. The stability of the reference gene is evaluated both individually and in groups of all possible combinations.ResultsHighly stable reference genes resulted in high Rt values regardless of the target gene used. The highest stability was achieved with a specific combination of 3 to 6 reference genes. A few genes were among the best reference genes across the cancer types studied here.ConclusioniRGvalid provides an easy and robust method to validate and identify the most stable reference gene or genes from a pool of candidate reference genes. The inclusivity of large expression data sets as well as the direct comparison of candidate reference genes makes it possible to identify reference genes with universal quality. This method can be used in any other gene expression studies when large cohorts of expression data are available.

Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage.

BackgroundThe borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC.ResultsGas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR.ConclusionThis study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC.

HEREDITARY LOAD IN MEAT AND EGG CHICKENS OF VARIOUS ORIGIN

The aim of the study was to determine the spectrum and frequency of hereditary genetic defects of embryo development in meat and egg hens of different genetic origin, obtained during an experiment to study the effectiveness of crossing roosters of imported meat crosses with meat and egg females of domestic selection. All embryos that died during egg incubation were carefully examined to detect morphopathology. The main research method is pathomorphological analysis of genetic defects of dead embryos. The spectrum and frequency of morphological and anatomical hereditary defects of embryos were established during pathological and anatomical examination of incubation waste. During the autopsy of dead embryos, morphological disorders in the structure of the skeleton were determined, as well as various disproportions of its individual parts.
 In the meat-egg hens of the original maternal form during three years of monitoring with the highest frequency (2.11–6.06%) revealed such a defect in embryo development as "donald duck". This indicates that the bird is "contaminated" with a "harmful gene" that causes this abnormality. It is worth noting that in groups of chickens that were artificially inseminated with the semen of roosters of meat crosses, this hereditary defect was also recorded. In the descendants of the first and second generations, this anomaly was absent, possibly due to its transition to a heterozygous state. Thus, we can conclude that the allele that expresses this lethal has in its genotype a bird of the local subpopulation "K". Only in meat and egg hens of domestic selection a wide variety of double anomalies was found – four species with a frequency of 1.05–1.12%. Most likely, double abnormalities are the result of homozygosity of dead embryos simultaneously for two lethal genes. Whereas, in chickens of other studied groups, only single anomalies of dead embryos were found, among them "exencephaly", "crossed beak", "shortened beak". Genetic defect of embryos "exencephaly" was found in chickens of most groups. It is obvious that the gene that determines the manifestation of this anomaly is significantly distributed in meat and egg hens of domestic selection and roosters used crosses. And in chickens of the created synthetic population "K-5" only this hereditary defect is revealed. In meat and egg hens of subpopulation "K" (F10) of the original maternal form and in the group of females, which were inseminated with polysperm of meat cocks of the cross "Cobb-500", with a low frequency (0.78–1.12%) a single "crossed beak" anomaly was found among the frozen embryos. This anomaly was not detected in the offspring of the first generation and in groups of chickens inseminated with semen of overripe brood stock. And only in the "cobb" bird of the "K-51" group among the hereditary defects of the dead embryos was this anomaly identified. In meat-egg hens of F10 subpopulation "K" with a low frequency (1.12%) was found a hereditary defect of embryos "shortened beak". Then this anomaly was found only in the "cobb" bird of both the first and second generation. The data show that the hereditary factor that determines this defect, the descendants inherited from the cocks of the cross "Cobb-500". The level of genetic burden in meat and egg hens of the local subpopulation "K", depending on the generation, ranged from 5.26 to 8.99% and was wavy in nature. In the descendants of the first generation it is low – 1.64–4.17%, in the "ross" crossbreeds is much smaller compared to the "cobb". The descendants of the second generation of different origins also had a low hereditary burden – in the range of 4.35–5.88%, which does not exceed the maximum allowable species value of 8.0%.
 The results of the research showed that crossing meat-egg hens of domestic selection with roosters of imported meat crosses "Cobb-500" and "Ross-308" did not lead to significant "contamination" of genotypes of F1-F2 offspring with lethal genes. This indicates a low share in the heredity of the used offspring of hidden carriers of "defective" genes. This may be due to the high selection of birds of foreign crosses, which does not contribute to the accumulation in its gene pool of lethal genes that cause embryonic developmental abnormalities. In chickens of the created synthetic population "K-5" the level of genetic burden is low (3.03%), which indicates the relative "purity" of this bird from lethal genes.

Functional pangenome analysis reveals high virulence plasticity of Aliarcobacter butzleri and affinity to human mucus

Aliarcobacter butzleri is an emerging pathogen that may cause enteritis in humans, however, the incidence of disease caused by this member of the Campylobacteriaceae family is still underestimated. Furthermore, little is known about the precise virulence mechanism and behavior during infection. Therefore, in the present study, through complementary use of comparative genomics and physiological tests on human gut models, we sought to elucidate the genetic background of a set of 32 A. butzleri strains of diverse origin and to explore the correlation with the ability to colonize and invade human intestinal cells in vitro.The simulated infection of human intestinal models showed a higher colonization rate in presence of mucus-producing cells. For some strains, human mucus significantly improved the resistance to physical removal from the in vitro mucosa, while short time-frame growth was even observed. Pangenome analysis highlighted a hypervariable accessory genome, not strictly correlated to the isolation source. Likewise, the strain phylogeny was unrelated to their shared origin, despite a certain degree of segregation was observed among strains isolated from different segments of the intestinal tract of pigs. The putative virulence genes detected in all strains were mostly encompassed in the accessory fraction of the pangenome. The LPS biosynthesis and in particular the chain glycosylation of the O-antigen is harbored in a region of high plasticity of the pangenome, which would indicate frequent horizontal gene transfer phenomena, as well as the involvement of this hypervariable structure in the adaptive behavior and sympatric evolution of A. butzleri.Results of the present study deepen the current knowledge on A. butzleri pangenome by extending the pool of genes regarded as virulence markers and provide bases to develop new diagnostic approaches for the detection of those strains with a higher virulence potential.

New Perspectives in Different Gene Expression Profiles for Early and Locally Advanced Non-Small Cell Lung Cancer Stem Cells.

IntroductionLung cancer is one of the most common cancers in the world, causing over 1.7 million deaths in 2018. Thus far, no effective treatments against lung cancer for advanced stages have been found. For early stages, although surgery is considered the gold standard treatment, 30–55% of patients develop recurrence within the first 5 years of surgery. Our aim is to assess whether cancer stem cells (CSC) display overexpression of a pool of genes that were previously identified for adenocarcinoma recurrence in patients with early and locally advanced stages of non-small cell lung cancer (NSCLC).MethodsThis cross-sectional study was carried out by harvesting surgical tumor specimens obtained from patients harboring early (I-II) and locally advanced (IIIA) stages of NSCLC. For each patient, cell sorting was performed to identify and isolate the ALDHhigh (CSC) and ALDHlow (cancer cells) populations. The mRNA expressions of 31 recurrence-related genes (target genes) in both ALDHhigh and ALDHlow populations were then assessed and compared.ResultsSurgical specimens were obtained from 22 patients harboring NSCLC. Sixteen (51.6%) out of 31 recurrence-related genes were significantly overexpressed in ALDHhigh cells in the early stages and 9 (29.0%) were overexpressed in the locally advanced stages of NSCLC. Overall, the relative mRNA expressions for these recurrence-related genes were higher in early-stage patients. The average fold change, considering all 31 recurrence-related genes together, was 4.5 (95% CI = 3.1-6.3) in early-stage patients and 1.6 (95% CI = 1.2-2.2) in locally advanced-stage patients.ConclusionsOur study represents the first attempt toward identifying genes associated with recurrence that are overexpressed in cancer stem cells in patients with early and locally advanced stages of NSCLC. This finding may contribute to the identification of new target therapies tailored for NSCLC stages.

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity.

The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of bacterial evolution. This is even more so if we consider that the mobilome of environmental bacteria can be the reservoir of genes that may later appear in the clinic. Recently, new genera have been proposed in the family Mycobacteriaceae , including the genus Mycolicibacterium , which encompasses dozens of species of agricultural, biotechnological, clinical and ecological importance, being ubiquitous in several environments. The current scenario in the Mycobacteriaceae mobilome has some bias because most of the characterized mycobacteriophages were isolated using a single host strain, and the few plasmids reported mainly relate to the genus Mycobacterium . To fill in the gaps in these issues, we performed a systematic in silico study of these mobile elements based on 242 available genomes of the genus Mycolicibacterium . The analyses identified 156 putative plasmids (19 conjugative, 45 mobilizable and 92 non-mobilizable) and 566 prophages in 86 and 229 genomes, respectively. Moreover, a contig was characterized by resembling an actinomycete integrative and conjugative element (AICE). Within this diversity of mobile genetic elements, there is a pool of genes associated with several canonical functions, in addition to adaptive traits, such as virulence and resistance to antibiotics and metals (mercury and arsenic). The type-VII secretion system was a common feature in the predicted plasmids, being associated with genes encoding virulent proteins (EsxA, EsxB, PE and PPE). In addition to the characterization of plasmids and prophages of the family Mycobacteriaceae , this study showed an abundance of these genetic elements in a dozen species of the genus Mycolicibacterium .

Metagenomic analysis of urban wastewater resistome and mobilome: A support for antimicrobial resistance surveillance in an endemic country.

In developing countries, where high levels of antimicrobial resistance are observed in hospitals, the surveillance of this phenomenon in wastewater treatment plants (WWTPs) and the environment is very limited, especially using cutting-edge culture-independent methods. In this study, the composition of bacterial communities, the resistome and mobilome (the pool of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), respectively) at a WWTP were determined using shotgun metagenomics and culture-based approaches. Wastewater samples were collected at four sampling points of a WWTP in Antioquia, Colombia. A total of 24 metagenomes were analyzed. Specifically, there were marked differences in bacterial community composition, resistome, and mobilome, according to the WWTP sampling points. Bacterial families of clinical importance such as Moraxellaceae, Aeromonadaceae, and Enterobacteriaceae were mainly detected in the WWTP influent and effluent samples. Genes encoding resistance to macrolide-lincosamide-streptogramin, β-lactams, and those conferring multidrug resistance (e.g., acrB, adeG, and mexD) were the most abundant. Moreover, some clinically important ARGs such as blaKPC-2 and blaCTX-M, and others not reported locally, such as blaTEM-196, blaGES-23, blaOXA-10, mcr-3, and mcr-5 were frequently detected. Co-occurrence network analyses indicated a significant association of ARGs such as blaOXA-58 and blaKPC genes with Aeromonadaceae and Enterobacteriaceae. Among the markers of MGEs, intI1 and ISCR8 were the most frequently detected. Altogether, this work reveals the importance of shotgun metagenomics and culture-based approaches in antimicrobial resistance studies. The findings also support that WWTPs are hotspots for antimicrobial resistance, whose analysis constitutes a powerful tool to predict the impact of antimicrobial resistance in a population.

Phenotypic and genotypic antimicrobial resistance patterns of Escherichia coli and Klebsiella isolated from dairy farm milk, farm slurry and water in Punjab, India

Antibiotic resistance is a mushrooming pandemic at national and international levels which if not controlled at this very moment, can lead to global problems. Main reason for emerging bacterial resistance is repeated exposure of bacteria to antimicrobial agents and access of bacteria to increasingly large pools of antimicrobial resistance genes in mixed bacterial populations. A total of 51 villages were sampled in the current study contributing to a total of 153 farms. A total of 612 samples comprising 153 each of raw pooled milk samples, slurry, animal drinking water and human drinking water were gathered from small, medium and large farms located in all seven tehsils of Ludhiana district of Punjab. In addition to that, 37 samples of village pond water were also collected from the targeted villages. Out of total 153 slurry, raw pooled milk samples, animal drinking water and human drinking water samples (each), the prevalence of 24.8%, 60%, 26.7% and 16.3% was found for E. coli respectively. On the other hand, for Klebsiella, the overall prevalence of 19.6%, 51%, 20.2% and 5.8% was found from slurry, raw pooled milk samples, animal drinking water and human drinking water respectively. In all matrices, the comparative frequency of resistance genes in positive isolates of E. coli and K. pneumoniae was: tetA > tetB > tetC, qnrS > qnrB > qnrA, sulII > sulI > sulIII. The highest proportion of resistance genes was found in slurry (193 genes) followed by milk (71 genes). The overall pattern of resistant genes was tetA > sulII > qnrS. In conclusion, data from the present study suggested that commensal E. coli and Klebsiella may act as reservoirs of antimicrobial drug resistance genes which may be mobilised into human populations and untreated animal waste may be considered an important source of resistant bacteria leading to environmental pollution.

BIOMEDICAL ENGINEERING OF SCLEROSTIN ACTION IN THE BONE REMODELING

Mathematical modeling of biological processes has bridged the fields of experimental as well as theoretical research and has carried forward remarkable innovation. Sclerostin is a fundamental communication element for bone remodeling and its activity regulates the reabsorption and deposition of new bone tissue. During this research, we have presented several studies, which illustrate the function of sclerostin in communication with the Wnt signaling pathways. This article features the sclerostin-based pathological patterns related to diseases such as bone cancer. To have a good remodeling process, the osteocytes must recruit the pre-osteoblast cells from the mesenchymal stem cells with the help of the signal mechanism given by the Wnt pathway. The Wnt signal pathway is a complex transduction of a pool of well-conserved genes whose expression regulates various activities like gene translation, cell adhesion, cell differentiation, mitogenic stimulation and polarity cell. The complexity of the interaction of the Wnt pathway is due to the ligands of Wnt itself, to the proteins R-spondin and norrin. The receptors on the surface of the cell, then, activate a process of transduction of the intracellular signal that initiates gene transduction. The hypothesis of a sort of “steady state” has therefore proved indispensable to establish a sort of common base on which the two phases. This paper seeks to give a qualitative view of the action of sclerostin through a simple mathematical model. We use a logic related to stimulation and inhibition signals of new tissue production and illustrate the role of sclerostin in the mechanical and biochemical interaction during the bone remodeling process.

Chapter 2 - Pituitary stalk interruption syndrome

Pituitary stalk interruption syndrome (PSIS) is a distinct developmental defect of the pituitary gland identified by magnetic resonance imaging and characterized by a thin, interrupted, attenuated or absent pituitary stalk, hypoplasia or aplasia of the adenohypophysis, and an ectopic posterior pituitary. The precise etiology of PSIS still remains elusive or incompletely confirmed in most cases. Adverse perinatal events, including breech delivery and hypoxia, were initially proposed as the underlying mechanism affecting the hypothalamic-pituitary axis. Nevertheless, recent findings have uncovered a wide variety of PSIS-associated molecular defects in genes involved in pituitary development, holoprosencephaly (HPE), neural development, and other important cellular processes such as cilia function. The application of whole exome sequencing (WES) in relatively large cohorts has identified an expanded pool of potential candidate genes, mostly related to the Wnt, Notch, and sonic hedgehog signaling pathways that regulate pituitary growth and development during embryogenesis. Importantly, WES has revealed coexisting pathogenic variants in a significant number of patients; therefore, pointing to a multigenic origin and inheritance pattern of PSIS. The disorder is characterized by inter- and intrafamilial variability and incomplete or variable penetrance. Overall, PSIS is currently viewed as a mild form of an expanded HPE spectrum. The wide and complex clinical manifestations include evolving pituitary hormone deficiencies (with variable timing of onset and progression) and extrapituitary malformations. Severe and life-threatening symptomatology is observed in a subset of patients with complete pituitary hormone deficiency during the neonatal period. Nevertheless, most patients are referred later in childhood for growth retardation. Prompt and appropriate hormone substitution therapy constitutes the cornerstone of treatment. Further studies are needed to uncover the etiopathogenesis of PSIS.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.

The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.

Genetic diversity analysis of grain yield and quality traits in rice germplasm accessions (Oryza sativa L.) by principal component analysis

The Rice germplasm provide with ample of genetic diversity and a treasury of valuable genes. It is a rich pool of important genes that plant breeders can exploit for crop improvement. Principal components with eigen values greater than 1 and variance level greater than 4 level is perceived to be the main PC. In this study, eight components exhibited Eigen values of >1 and showed cumulative variation of 75.22%. The first PC (15.83%) and second PC (15.33%) showed for cumulative variation 31.36%. The PC1 recorded 15.83%, although PC2, PC3, PC4, PC5, PC6, PC7 and PC8 displayed 15.33%, 12.64%, 9.03%, 7.4%, 5.91%, 4.61% and 4.27% variance respectively between the accessions for the characters in analysis. Genotypes Saraiphool, MTU 1010, Zinc rice-2, Chaptimathyala, Bora, Korma, R-RKM-1, Kalajeera, Jauphool, Tiltaturi and Parwatkala were found to be promising and found to be genetically divergent. Hence, these genotypes could be utilized in the hybridization programme to produce transgressive segregants.

Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics.

Mammary carcinoma, including triple-negative breast carcinomas (TNBC) are tumor-types for which human and canine pathologies are closely related at the molecular level. The efficacy of an oncolytic vaccinia virus (VV) was compared in low-passage primary carcinoma cells from TNBC versus non-TNBC. Non-TNBC cells were 28 fold more sensitive to VV than TNBC cells in which VV replication is impaired. Single-cell RNA-seq performed on two different TNBC cell samples, infected or not with VV, highlighted three distinct populations: naïve cells, bystander cells, defined as cells exposed to the virus but not infected and infected cells. The transcriptomes of these three populations showed striking variations in the modulation of pathways regulated by cytokines and growth factors. We hypothesized that the pool of genes expressed in the bystander populations was enriched in antiviral genes. Bioinformatic analysis suggested that the reduced activity of the virus was associated with a higher mesenchymal status of the cells. In addition, we demonstrated experimentally that high expression of one gene, DDIT4, is detrimental to VV production. Considering that DDIT4 is associated with a poor prognosis in various cancers including TNBC, our data highlight DDIT4 as a candidate resistance marker for oncolytic poxvirus therapy. This information could be used to design new generations of oncolytic poxviruses. Beyond the field of gene therapy, this study demonstrates that single-cell transcriptomics can be used to identify cellular factors influencing viral replication.

The Crosstalk between Cytokinin and Auxin Signaling Pathways in the Control of Natural Senescence of Arabidopsis thaliana Leaves

Natural senescence of leaves is a regular physiological process subjected to a certain genetic program and controlled by various phytohormones. Cytokinins (CKs) play a crucial role in the leaf-senescence control being negative regulators of this process. We previously reported on the prolonged vegetative growth and the development of a double knockout ahk2ahk3 mutant of Arabidopsis thaliana Heynh. (L.) for the genes encoding CK receptors. According to the data of the transcriptomic analysis and real-time RT‑PCR of selected genes performed in this study, the delay of leaf senescence in ahk2ahk3 mutants is accompanied by enhanced (4–281-fold) expression of the group of SAUR (small auxin-up RNA) genes encoding auxin response proteins and by upregulation of the SSPP (senescence-suppressed protein phosphatase) gene, whose expression level significantly (137-fold) exceeded that in a wild-type transcriptome. Thus, it is quite possible that under significant inhibition of the CK signaling leaf senescence in Arabidopsis plants regulated via a compensatory mechanism connected with changes in the expression of the SAUR gene family and a certain pool of genes related to the auxin transport and signaling.

Genetic Characterization of Multiple Antibiotics Resistance Genes of Escherichia coli Strain from Cow Milk and Its Products Sold in Abuja, Nigeria

Background: Antibiotic resistance has remained a global concern. Food pathogens that carry resistance genes will cause public health threat irrespective of their pathogenicity, as this pool of resistance genes are disseminated via food chain. The antibiotic susceptibility of E. coli isolates to different antibiotics were investigated and resistance genes were genetically identified by multiplex Polymerase Chain Reaction (PCR). The study aimed to determine the phenotypic antibiotic resistance pattern of the E. coli isolates and characterize the antibiotics resistance genes in the E. coli isolates from the Cow milk and milk products.
 Results: The study showed that the E. coli isolates were Multidrug resistant (MDR) to several antibiotics with resistance pattern of four to ten combinations of antibiotics and the antibiotics resistance occurred mostly in three classes of antibiotics, namely: β-lactams, Amphenicol and Tetracycline. The antibiotics resistance genes expressed in the multidrug resistant E. coli isolates were tetA 22(78.6%), dfrA1 9(32.1%), blaCITM and blaSHV 3(10.7%), tetB and blaTEM 1(3.6%), qnr 0(0%) and aac (3)-iv 0(0%).
 Conclusion: The study showed that the cow milk and its products sold on the streets of Abuja are contaminated with resistant E. coli that can pose health risk to the consumers. Monitoring and screening for resistant food pathogens in food especially of animal origin is vital to mitigate the prevalence of antibiotics resistance.

Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics.

Shigella flexneri is the causative agent of dysentery. For pathogens, iron is a critical micronutrient as its bioavailability is usually low in bacterial niches. This metal is involved in critical physiological processes mainly as a component of important metabolic molecules involved in redox reactions. Usually bacteria respond to fluctuations in iron availability to regulate iron acquisition and other iron-related functions. Recently the close metabolic feedback between iron and riboflavin, another pivotal biological redox agent, began to draw attention in bacteria. This is a widespread biological phenomenon, partly characterized by the coordination of regulatory responses to iron and riboflavin, probably owed to the involvement of these cofactors in common processes. Nonetheless, no systematic analyses to determine the extent of this regulatory effect have been performed in any species. Here, the transcriptomics responses to iron, riboflavin, iron in the presence of riboflavin and riboflavin in the presence of iron were assessed and compared in S. flexneri. The riboflavin regulon had a 43% overlap with the iron regulon. Notably, the presence of riboflavin highly increased the number of iron-responsive genes. Reciprocally, iron drastically changed the pool of riboflavin-responsive genes. Gene ontology (GO) functional terms enrichment analysis showed that biological processes were distinctively enriched for each subgroup of responsive genes. Among the biological processes regulated by iron and riboflavin were iron uptake, amino acids metabolism and electron transfer for ATP synthesis. Thus, iron and riboflavin highly affect the transcriptomics responses induced by each other in S. flexneri. GO terms analysis suggests that iron and riboflavin coordinately regulate specific physiological functions involving redox metabolism.

Studies on Bd0934 and Bd3507, Two Secreted Nucleases from Bdellovibrio bacteriovorus, Reveal Sequential Release of Nucleases during the Predatory Cycle.

Bdellovibrio bacteriovorus is an obligate predatory bacterium that invades and kills a broad range of Gram-negative prey cells, including human pathogens. Its potential therapeutic application has been the subject of increased research interest in recent years. However, an improved understanding of the fundamental molecular aspects of the predatory life cycle is crucial for developing this bacterium as a "living antibiotic." During intracellular growth, B. bacteriovorus secretes an arsenal of hydrolases, which digest the content of the host cell to provide growth nutrients for the predator, e.g., prey DNA is completely degraded by the nucleases. Here, we have, on a genetic and molecular level, characterized two secreted DNases from B. bacteriovorus, Bd0934 and Bd3507, and determined the temporal expression profile of other putative secreted nucleases. We conclude that Bd0934 and Bd3507 are likely a part of the predatosome but are not essential for the predation, host-independent growth, prey biofilm degradation, and self-biofilm formation. The detailed temporal expression analysis of genes encoding secreted nucleases revealed that these enzymes are produced in a sequential orchestrated manner. This work contributes to our understanding of the sequential breakdown of the prey nucleic acid by the nucleases secreted during the predatory life cycle of B. bacteriovorusIMPORTANCE Antibiotic resistance is a major global concern with few available new means to combat it. From a therapeutic perspective, predatory bacteria constitute an interesting tool. They not only eliminate the pathogen but also reduce the overall pool of antibiotic resistance genes through secretion of nucleases and complete degradation of exogenous DNA. Molecular knowledge of how these secreted DNases act will give us further insight into how antibiotic resistance, and the spread thereof, can be limited through the action of predatory bacteria.

Side effects of free nitrous acid on the sewer resistome and mobilome

The dosage of free nitrous acid (FNA) is an effective treatment to control emissions of hydrogen sulfide and methane from sewers. It is unclear, however, whether its application could affect the sewer resistome and mobilome (the pool of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), respectively). Here, a lab-scale assay for FNA treatment (60 ppm for 6 h) was conducted to explore its effects on the abundance of ARGs and MEGs among sewer compartments (i.e., suspended cells and biofilms) using shotgun metagenomics. FNA treatment caused a significant reduction in viable cells (≈25%, p < 0.01), a 75% and a 83% reduction in the abundance of Aeromonadaceae and Moraxellaceae, respectively, and a 50% increase for Campylobacteraceae in the suspended cell fraction whereas bacterial communities in sewer biofilms remained unaltered. Comparative analyses before and after the FNA treatment also showed a significant reduction (p < 0.01) in the relative abundance of ARGs in the suspended cell fraction, particularly for genes conferring resistance to multidrug, macrolide-lincosamide-streptogramin B, quinolones and bacitracin. Besides, the relative abundance of mobile ISCR8 element significantly decreased (from 0.014% to 0.010%) whereas genes conferring resistance to glycopeptides significantly increased (from 0.0008% to 0.0016%) after 6 h of treatment. A heatmap analysis also showed a clear reduction in the relative abundance of genes conferring resistance to β-lactam antibiotics and multidrug resistance. The observed reduction in the relative abundance of ARGs and MGEs in suspended cells is a beneficial side effect of a treatment originally intended to mitigate emissions of noxious gases from sewers and may be helpful to guide future policy recommendations to lessen the spread of antibiotic resistance across the urban water cycle.