The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents ...one of the most important and studied mechanisms used by plant growth-promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly ...determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada’s Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus. We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195–135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45–21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.
Conspectus The development of robust methods allowing the precise detection of specific nucleic acid sequences is of major societal relevance, paving the way for significant advances in biotechnology ...and biomedical engineering. These range from a better understanding of human disease at a molecular level, allowing the discovery and development of novel biopharmaceuticals and vaccines, to the improvement of biotechnological processes providing improved food quality and safety, efficient green fuels, and smart textiles. Among these applications, the significance of pathogen diagnostics as the main focus of this Account has become particularly clear during the recent SARS-CoV-2 pandemic. In this context, while RT-PCR is the gold standard method for unambiguous detection of genetic material from pathogens, other isothermal amplification alternatives circumventing rapid heating–cooling cycles up to ∼95 °C are appealing to facilitate the translation of the assay into point-of-care (PoC) analytical platforms. Furthermore, the possibility of routinely multiplexing the detection of tens to hundreds of target sequences with single base pair specificity, currently not met by state-of-the-art methods available in clinical laboratories, would be instrumental along the path to tackle emergent viral variants and antimicrobial resistance genes. Here, we advocate that padlock probes (PLPs), first reported by Nilsson et al. in 1994, coupled with rolling circle amplification (RCA), termed here as PLP-RCA, is an underexploited technology in current arena of isothermal nucleic acid amplification tests (NAATs) providing an unprecedented degree of multiplexing, specificity, versatility, and amenability to integration in miniaturized PoC platforms. Furthermore, the intrinsically digital amplification of PLP-RCA retains spatial information and opens new avenues in the exploration of pathogenesis with spatial multiomics analysis of infected cells and tissue. The Account starts by introducing PLP-RCA in a nutshell focusing individually on the three main assay steps, namely, (1) PLP design and ligation mechanism, (2) RCA after probe ligation, and (3) detection of the RCA products. Each subject is touched upon succinctly but with sufficient detail for the reader to appreciate some assay intricacies and degree of versatility depending on the analytical challenge at hand. After familiarizing the reader with the method, we discuss specific examples of research in our group and others using PLP-RCA for viral, bacterial, and fungal diagnostics in a variety of clinical contexts, including the genotyping of antibiotic resistance genes and viral subtyping. Then, we dissect key developments in the miniaturization and integration of PLP-RCA to minimize user input, maximize analysis throughput, and expedite the time to results, ultimately aiming at PoC applications. These developments include molecular enrichment for maximum sensitivity, spatial arrays to maximize analytical throughput, automation of liquid handling to streamline the analytical workflow in miniaturized devices, and seamless integration of signal transduction to translate RCA product titers (and ideally spatial information) into a readable output. Finally, we position PLP-RCA in the current landscape of NAATs and furnish a systematic Strengths, Weaknesses, Opportunities and Threats analysis to shine light upon unpolished edges to uncover the gem with potential for ubiquitous, precise, and unbiased pathogen diagnostics.
► Antioxidants tested would be beneficial for reducing the velocity of lipid oxidation. ► Herbs and honey exhibited great efficacy on preventing formation of hexanal. ► The sensory evaluation ...indicated that herbs and honey resulted in a pleasant flavour.
The effect of combinations of sage, oregano and honey on lipid oxidation in cooked chicken meat during refrigeration at 4°C for 96h was determined. Chicken samples (thigh and breast) were then separated into five groups: control; butylated hydroxytoluene; oregano+sage; oregano+sage+5%honey and oregano+sage+10%honey. Quantitative measurements of thiobarbituric acid reactive substances, conjugated dienes, hexanal, fatty acids, cholesterol and cholesterol oxides were used as indicators of lipid oxidation. Acceptability and preference were also evaluated. The effectiveness of the natural antioxidants for reducing the velocity of lipid oxidation in cooked chicken thigh and breast was demonstrated after 48 and 96h of refrigeration at 4°C. The treatments that presented the lowest hexanal values after 96h of refrigeration were oregano+sage+5%honey and oregano+sage+10%honey. Only traces of free cholesterol oxides were found (25-OH, 7-k, 7α-OH and 7β-OH). The natural antioxidants protected cooked chicken meat from oxidation processes and resulted in great acceptability.
Food-borne illnesses are a growing concern for the food industry and consumers, with millions of cases reported every year. Consequently, there is a critical need to develop rapid, sensitive, and ...inexpensive techniques for pathogen detection in order to mitigate this problem. However, current pathogen detection strategies mainly include time-consuming laboratory methods and highly trained personnel. Electrochemical in-field biosensors offer a rapid, low-cost alternative to laboratory techniques, but the electrodes used in these biosensors require expensive nanomaterials to increase their sensitivity, such as noble metals (e.g., platinum, gold) or carbon nanomaterials (e.g., carbon nanotubes, or graphene). Herein, we report the fabrication of a highly sensitive and label-free laser-induced graphene (LIG) electrode that is subsequently functionalized with antibodies to electrochemically quantify the food-borne pathogen Salmonella enterica serovar Typhimurium. The LIG electrodes were produced by laser induction on the polyimide film in ambient conditions and, hence, circumvent the need for high-temperature, vacuum environment, and metal seed catalysts commonly associated with graphene-based electrodes fabricated via chemical vapor deposition processes. After functionalization with Salmonella antibodies, the LIG biosensors were able to detect live Salmonella in chicken broth across a wide linear range (25 to 105 CFU mL–1) and with a low detection limit (13 ± 7 CFU mL–1; n = 3, mean ± standard deviation). These results were acquired with an average response time of 22 min without the need for sample preconcentration or redox labeling techniques. Moreover, these LIG immunosensors displayed high selectivity as demonstrated by nonsignificant response to other bacteria strains. These results demonstrate how LIG-based electrodes can be used for electrochemical immunosensing in general and, more specifically, could be used as a viable option for rapid and low-cost pathogen detection in food processing facilities before contaminated foods reach the consumer.
Development of ketosis in high-producing dairy cows contributes to several animal health issues and highlights the need for a better understanding of the genetic basis of metabolic diseases. To ...evaluate the pattern of differential gene expression in the liver of cows under negative energy balance (NEB), and under subclinical and clinical ketosis, a meta-analysis of gene expression and genome-wide association studies results was performed. An initial systematic review identified 118 articles based on the key words “cow,” “liver,” “negative energy balance,” “ketosis,” “expression,” “qPCR,” “microarray,” “proteomic,” “RNA-Seq,” and “GWAS.” After further screening for only peer-reviewed and pertinent articles for gene expression during NEB and clinical and subclinical ketosis (considering plasma levels of β-hydroxybutyrate), 20 articles were included in the analysis. From the systematic review, 430 significant SNPs identified by genome-wide association studies (GWAS) were assigned to genes reported in gene expression studies by considering chromosome and base pair positions in the ARS-UCD 1.2 bovine assembly. Venn diagrams were created to integrate the data obtained in the systematic review, and Gene Ontology enrichment analysis was carried out using official gene names. A QTL enrichment analysis was also performed to identify potential positional candidate loci. Twenty-four significant SNPs were located within the coordinates of differentially expressed genes located on chromosomes 2, 3, 6, 9, 11, 14, 27, and 29. Three significant metabolic pathways were associated with NEB and subclinical and clinical ketosis. In addition, 2 important genes, PPARA (peroxisome proliferator activated receptor alpha) and ACACA (acetyl-coenzyme A carboxylase α), were identified, which were differentially expressed in the 3 metabolic conditions. The PPARA gene is involved in the regulation of lipid metabolism and fatty liver disease and the ACACA gene encodes an enzyme that catalyzes the carboxylation of acetyl-coenzyme A to malonyl-coenzyme A, which is a rate-limiting step in fatty acid synthesis. Gene network analysis revealed co-expression interactions among 34 genes associated with functions involving fatty acid transport and fatty acid metabolism. For the annotated QTL, 9 QTL were identified for ketosis. The genes FN1 (fibronectin 1) and PTK2 (protein tyrosine kinase 2), which are mainly involved in cell adhesion and formation of extracellular matrix constituents, were enriched for QTL previously associated with the trait “ketosis” on chromosome 2 and for the trait “milk iron content” on chromosome 14, respectively. This integration of gene expression and GWAS data provides an additional understanding of the genetic background of NEB and subclinical and clinical ketosis in dairy cattle. Thus, it is a useful approach to identify biological mechanisms underlying these metabolic conditions in dairy cattle.
This paper develops a model where reductions in mortality are the main force behind economic development. The model generates a pattern of changes similar to the demographic transition, where gains ...in life expectancy at birth are followed by reductions infertility and increases in the rate of human capital accumulation. The onset of the transition is characterized by a critical level of life expectancy at birth, which marks the movement of the economy from a Malthusian equilibrium to an equilibrium with investments in human capital and the possibility of long-run growth.
Microfluidics has emerged rapidly over the past 20 years and has been investigated for a variety of applications from life sciences to environmental monitoring. Although continuous-flow microfluidics ...is ubiquitous, segmented-flow or droplet microfluidics offers several attractive features. Droplets can be independently manipulated and analyzed with very high throughput. Typically, microfluidics is carried out within planar networks of microchannels, namely, microfluidic chips. We propose that fibers offer an interesting alternative format with key advantages for enhanced optical coupling. Herein, we demonstrate the generation of monodisperse droplets within a uniaxial optofluidic Lab-in-a-Fiber scheme. We combine droplet microfluidics with laser-induced fluorescence (LIF) detection achieved through the development of an optical side-coupling fiber, which we term a periscope fiber. This arrangement provides stable and compact alignment. Laser-induced fluorescence offers high sensitivity and low detection limits with a rapid response time making it an attractive detection method for in situ real-time measurements. We use the well-established fluorophore, fluorescein, to characterize the Lab-in-a-Fiber device and determine the generation of Formula: see text 0.9 nL droplets. We present characterization data of a range of fluorescein concentrations, establishing a limit of detection (LOD) of 10 nM fluorescein. Finally, we show that the device operates within a realistic and relevant fluorescence regime by detecting reverse-transcription loop-mediated isothermal amplification (RT-LAMP) products in the context of COVID-19 diagnostics. The device represents a step towards the development of a point-of-care droplet digital RT-LAMP platform.
Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile ...invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.
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