To effectively monitor biodegrading populations, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the 2,402 known genes and pathways involved in biodegradation and metal resistance. This array contained 1,662 unique and group-specific probes with <85% similarity to their nontarget sequences. Based on artificial probes, our results showed that under hybridization conditions of 50°C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. The detection limit was ϳ5 to 10 ng of genomic DNA in the absence of background DNA and 50 to 100 ng of pure-culture genomic DNA in the presence of background DNA or 1.3 ؋ 10 7 cells in the presence of background RNA. Strong linear relationships between the signal intensity and the target DNA and RNA were observed (r 2 ‫؍‬ 0.95 to 0.99). Application of this type of microarray to analyze naphthalene-amended enrichment and soil microcosms demonstrated that microflora changed differently depending on the incubation conditions. While the naphthalene-degrading genes from Rhodococcus-type microorganisms were dominant in naphthalene-degrading enrichments, the genes involved in naphthalene (and polyaromatic hydrocarbon and nitrotoluene) degradation from gram-negative microorganisms, such as Ralstonia, Comamonas, and Burkholderia, were most abundant in the soil microcosms. In contrast to general conceptions, naphthalene-degrading genes from Pseudomonas were not detected, although Pseudomonas is widely known as a model microorganism for studying naphthalene degradation. The real-time PCR analysis with four representative genes showed that the microarray-based quantification was very consistent with real-time PCR (r 2 ‫؍‬ 0.74). In addition, application of the arrays to both polyaromatic-hydrocarbon-and benzene-toluene-ethylbenzene-xylene-contaminated and uncontaminated soils indicated that the developed microarrays appeared to be useful for profiling differences in microbial community structures. Our results indicate that this technology has potential as a specific, sensitive, and quantitative tool in revealing a comprehensive picture of the compositions of biodegradation genes and the microbial community in contaminated environments, although more work is needed to improve detection sensitivity.The transformation of environmental contaminants is a complex process that is influenced by the nature and amount of the contaminant present, the structure and dynamics of the indigenous microbial community, and the interplay of geochemical and biological factors at contaminated sites (1,14,26,36). A better understanding of the processes inherent in natural bioremediation requires, in part, a better understanding of microbial ecology. However, conventional molecular methods (PCR-based technologies, such as gene cloning, terminal-restriction fragment len...

The availability of the complete genome sequence for Shewanella oneidensis MR-1 has permitted a comprehensive characterization of the ferric uptake regulator (Fur) modulon in this dissimilatory metal-reducing bacterium. We have employed targeted gene mutagenesis, DNA microarrays, proteomic analysis using liquid chromatography-mass spectrometry, and computational motif discovery tools to define the S. oneidensis Fur regulon. Using this integrated approach, we identified nine probable operons (containing 24 genes) and 15 individual open reading frames (ORFs), either with unknown functions or encoding products annotated as transport or binding proteins, that are predicted to be direct targets of Fur-mediated repression. This study suggested, for the first time, possible roles for four operons and eight ORFs with unknown functions in iron metabolism or iron transport-related functions. Proteomic analysis clearly identified a number of transporters, binding proteins, and receptors related to iron uptake that were up-regulated in response to a fur deletion and verified the expression of nine genes originally annotated as pseudogenes. Comparison of the transcriptome and proteome data revealed strong correlation for genes shown to be undergoing large changes at the transcript level. A number of genes encoding components of the electron transport system were also differentially expressed in a fur deletion mutant. The gene omcA (SO1779), which encodes a decaheme cytochrome c, exhibited significant decreases in both mRNA and protein abundance in the fur mutant and possessed a strong candidate Fur-binding site in its upstream region, thus suggesting that omcA may be a direct target of Fur activation.

Human infections of H5N1 highly pathogenic avian influenza virus have continued to occur in

Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe 2؉ acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the ␦-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.The underground corrosion of metal pipes used for gas or water and the generation of sulfide during digestion of domestic and agricultural wastes have been the economic and environmental processes that have historically driven the desire to understand the metabolism of sulfate-reducing bacteria (SRB) (16). The SRB have been a particular problem for the petroleum industry due to their roles in metal corrosion, petroleum souring, and the health hazards of hydrogen sulfide. In contrast, SRB can be advantageous for bioremediation processes. A variety of studies (6,15,17,33,39) have...

The outbreak of 2019-nCoV pneumonia in the city of Wuhan, China has resulted in more than 70,000 laboratory confirmed cases, and recent studies showed that 2019-nCoV (SARS-CoV-2) could be of bat origin but involve other potential intermediate hosts. In this study, we assembled the genomes of coronaviruses identified in sick pangolins. The molecular and phylogenetic analyses showed that pangolin Coronaviruses (pangolin-CoV) are genetically related to both the 2019-nCoV and bat Coronaviruses but do not support the 2019-nCoV arose directly from the pangolin-CoV. Our study also suggested that pangolin be natural host of Betacoronavirus, with a potential to infect humans. Large surveillance of coronaviruses in pangolins could improve our understanding of the spectrum of coronaviruses in pangolins. Conservation of wildlife and limits of the exposures of humans to wildlife will be important to minimize the spillover risks of coronaviruses from wild animals to humans. author/funder. All rights reserved. No reuse allowed without permission.

Background The full impact of COVID‐19 on pregnancy remains uncharacterized. Current literature suggests minimal maternal, fetal, and neonatal morbidity and mortality. 1 COVID‐19 manifestations appear similar between pregnant and non‐pregnant women. 2 Objectives/Study Design We present a case of placental SARS‐CoV‐2 virus in a woman with mild COVID‐19 disease, then review the literature. RT‐PCR was performed to detect SARS‐CoV‐2. Immunohistochemistry staining was performed with specific monoclonal antibodies to detect SARS‐CoV‐2 antigen or to identify trophoblasts. Results A 29 year‐old multigravida presented at 40‐4/7 weeks for labor induction. With myalgias two days prior, she tested positive for SARS‐CoV‐2. We demonstrate maternal vascular malperfusion, with no fetal vascular malperfusion, as well as SARS‐CoV‐2 virus in chorionic villi endothelial cells, and also rarely in trophoblasts. Conclusions To our knowledge, this is the first report of placental SARS‐CoV‐2 despite mild COVID‐19 disease (no symptoms of COVID‐19 aside from myalgias); patient had no fever, cough, or shortness of breath, but only myalgias and sick contacts. Despite her mild COVID‐19 disease in pregnancy, we demonstrate placental vasculopathy and presence of SARS‐CoV‐2 virus across the placenta. Evidence of placental COVID‐19 raises concern for placental vasculopathy (potentially leading to fetal growth restriction and other pregnancy complications) and possible vertical transmission – especially for pregnant women who may be exposed to COVID‐19 in early pregnancy. This raises important questions of whether future pregnancy guidance should include stricter pandemic precautions, such as screening for a wider array of COVID‐19 symptoms, increased antenatal surveillance, and possibly routine COVID‐19 testing throughout pregnancy. This article is protected by copyright. All rights reserved.

Background: Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported.

Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage bias helps understand evolution of living organisms. A codon usage bias pipeline is demanding for codon usage bias analyses within and across genomes. Here we present a CodonO webserver service as a user-friendly tool for codon usage bias analyses across and within genomes in real time. The webserver is available at http//www.sysbiology.org/CodonO. Contact: wanhenry@yahoo.com.