Search

Acetate utilization and macromolecule synthesis during sporulation (meiosis) of Saccharomyces cerevisiae were studied. When diploid cells are transferred from glucose nutrient medium to acetate sporulation medium at early stationary phase, respiration of the exogenously supplied acetate proceeds without any apparent lag. At the completion of ascospore development, 62% of the acetate carbon consumed has been respired, 22% remains in the soluble pool, and 16% is incorporated into lipids, protein, nucleic acids, and other cell components. Measurements of the rate of protein synthesis during sporulation reveal two periods of maximal synthetic activity: an early phase coincidental with increases in deoxyribonucleic acid, ribonucleic acid, and protein cellular content and a later phase during ascospore formation. Experiments in which protein synthesis was inhibited at intervals during sporulation indicate that protein synthesis is required both for the initiation and completion of ascus development.

An active, cell-free protein synthesizing system has been obtained from yeast mitochondria. The system is stimulated by both polyuridylate and R17 RNA and is sensitive to inhibitors of bacterial protein synthesizing systems. A comparison is made between this system and that found in the cytoplasm of yeast.

Experiments were carried out to determine whether, during outgrowth of bacterial spores, deoxyribonucleic acid (DNA) replication provided the basis by which ordered transcription was controlled. During outgrowth, significant DNA synthesis does not occur until just prior to the onset of cell division. However, incorporation of radioactive DNA precursors into DNA is observed within 5 to 10 min after the initiation of germination. By employing a thymine-requiring auxotroph and (3)H-bromodeoxyuridine, this incorporation appears to be a result of DNA replication and not repair synthesis. For the following reasons it was concluded that, during outgrowth, transcriptional processes were not ordered by DNA replication. (i) In a thymine auxotroph, thymine addition did not alter the periodicity of induced alpha-glucosidase and histidase synthesis during outgrowth. (ii) DNA synthesis was inhibited 80% by 5-fluoro-2'-deoxyuridine (FUdR), and, after a 5-min lag, completely by mitomycin C, but these inhibitors exerted a differential effect on induced histidase synthesis. Enzyme synthesis was insensitive to FUdR but was inhibited by mitomycin C, presumably as a result of cross-linking of the complementary DNA strands.

Keynan, A. (University of Wisconsin, Madison) and H. O. Halvorson. Calcium dipicolinic acid-induced germination of Bacillus cereus spores. J. Bacteriol. 83:100-105. 1962.-The germination of spores of Bacillus cereus strain T can be initiated by calcium dipicolinic acid. The kinetics of germination are characterized by a long lag period followed by a rapid loss of refractility. The lag period displays the temperature dependence of a metabolic reaction, whereas the rate of germination is relatively independent of temperature. Germination induced by calcium dipicolinic acid is insensitive to l-alanine analogues, is sensitive to metabolic poisons, and proceeds without a detectable activation stage. It was concluded that calcium dipicolinic acid-induced germination has a metabolic basis and differs, at least in its initial phases, from l-alanine-induced germination.

McCormick, Neil G. (University of Wisconsin, Madison), and Harlyn O. Halvorson. Purification and properties of l-alanine dehydrogenase from vegetative cells of Bacillus cereus. J. Bacteriol. 87:68-74. 1964.-The l-alanine dehydrogenase from vegetative cells of Bacillus cereus strain T has been purified approximately 200-fold. The enzyme has a molecular weight of 248,000 and a turnover number of 80,000 moles of substrate per min per mole of enzyme. The Michaelis constants for the substrates and the equilibrium constant for the reaction catalyzed by this enzyme are in close agreement with reported values for other l-alanine dehydrogenases. The kinetic properties of the enzyme purified from vegetative cells are identical to those of the enzyme isolated from spores of the same organism, but differ with respect to relative heat stability. Whereas spores contain a heat-resistant enzyme, vegetative cells contain, in addition, a heat-sensitive enzyme. No evidence was found to support the hypothesis that a molecular conversion type of phenomenon plays a role in the appearance of spore enzyme.

Two deoxyribonucleic acid (DNA)-dependent ribonucleic acid (RNA) polymerases (I, II) have been solubilized from isolated Saccharomyces cerevisiae nuclei. The enzymes can be separated by chromatography on O-diethylaminoethyl Sephadex. Both enzymes are active with high-molecular-weight nuclear yeast DNA, although RNA polymerase I has a higher affinity for polydeoxy-adenylic-thymidylic acid and RNA polymerase II for denatured DNA. RNA polymerase I is active only with manganese. alpha-Amanitin inhibits only the activity of RNA polymerase II.

The study of sporulation in Saccharomyces cerevisiae is complicated by the fact that not all cells in the population complete sporulation and that the kinetics of development of those which do are not synchronous. By separating vegetative cells by zonal rotor centrifugation into fractions of increasing cell volume and hence progressive stages of the vegetative cell cycle, it was possible to observe sporulation of more homogeneous, synchronous populations. The capacity of S. cerevisiae to complete sporulation is low for small single cells at the beginning of the cell cycle and is greatest for large budded cells about to divide. The capacity of a cell to complete sporulation thus appears to be directly related to the stage in the vegetative cell cycle from which it was taken. The use of synchronously sporulating cultures made it possible to examine very early decision events leading to the commitment of a cell to sporulation. In addition, differences in the capacity of a mother and daughter cell produced by cell scission were examined.

MacQuillan, Anthony M. (University of Wisconsin, Madison) and Harlyn O. Halvorson. Metabolic control of beta-glucosidase synthesis in yeast. J. Bacteriol. 84:23-30. 1962-The hybrid Saccharomyces fragilis x S. dobzhanskii produced a constitutive beta-glucosidase when grown in succinate synthetic medium. Upon addition of beta-glucosides, thio-beta-glucosides, or low concentrations of glucose, a further induction of enzyme synthesis was observed. Studies with other sugars revealed some specificity in response to hexose induction. Phenyl-thio-beta-d-glucoside did not affect constitutive synthesis nor induction by glucosides, thio-glucosides, or glucose. Repression of beta-glucosidase synthesis is brought about by high concentrations of glucose and other carbon compounds. Preinduction does not confer resistance to catabolic repression of enzyme synthesis; this leads to the conclusion that two sites of control for beta-glucosidase synthesis are present in yeast. Multiplicity of control is further suggested from: (i) the properties of the inducing system; (ii) semiconstitutive nature of enzyme synthesis; (iii) the repression of constitutive synthesis by glucose; (iv) the elevated derepressed rates of enzyme synthesis after glucose inhibition; and (v) the selection of a family of low constitutive mutants with variable inducibility.

Tauro, Patric (The University of Wisconsin, Madison), and Harlyn O. Halvorson. Effect of gene position on the timing of enzyme synthesis in synchronous cultures of yeast. J. Bacteriol. 92:652-661.-In synchronously growing cultures of Saccharomyces cerevisiae, enzyme synthesis is periodic. The effect of various factors on the timing of alpha-glucosidase synthesis has been investigated. The period of the cell cycle during which alpha-glucosidase is synthesized is unaffected by the method employed to induce synchrony, as well as other environmental conditions. However, a definite relationship exists between the number of nonallelic structural genes present for alpha-glucosidase and the number of periods of synthesis during the cell cycle. It is concluded that the periodic synthesis of enzymes observed in synchronously growing cultures of yeast is probably the result of an ordered process of transcription of the various structural genes.

Background: The Pacific oyster, Crassostrea gigas, is an economically important shellfish around the world. Great efforts have been made to improve its growth rate through genetic breeding. However, the candidate marker genes, pathways, and potential lncRNAs involved in oyster growth regulation remain largely unknown. To identify genes, lncRNAs, and pathways involved in growth regulation, C. gigas spat was cultured at a low temperature (15 ℃) to yield a growth-inhibited model, which was used to conduct comparative transcriptome analysis with spat cultured at normal temperature (25 ℃). Results: In total, 8627 differentially expressed genes (DEGs) and 1072 differentially expressed lncRNAs (DELs) were identified between the normal-growth oysters (cultured at 25 ℃, hereinafter referred to as NG) and slow-growth oysters (cultured at 15 ℃, hereinafter referred to as SG). Functional enrichment analysis showed that these DEGs were mostly enriched in the AMPK signaling pathway, MAPK signaling pathway, insulin signaling pathway, autophagy, apoptosis, calcium signaling pathway, and endocytosis process. LncRNAs analysis identified 265 cis-acting pairs and 618 trans-acting pairs that might participate in oyster growth regulation. The expression levels of LNC_001270, LNC_003322, LNC_011563, LNC_006260, and LNC_012905 were inducible to the culture temperature and food abundance. These lncRNAs were located at the antisense, upstream, or downstream of the SREBP1/p62, CDC42, CaM, FAS, and PIK3CA genes, respectively. Furthermore, the expression of the trans-acting lncRNAs, including XR_9000022.2, LNC_008019, LNC_015817, LNC_000838, LNC_00839, LNC_011859, LNC_007294, LNC_006429, XR_002198885.1, and XR_902224.2 was also significantly associated with the expression of genes enriched in AMPK signaling pathway, insulin signaling pathway, autophagy, apoptosis, calcium signaling pathway, and endocytosis process. Conclusions: In this study, we identified the critical growth-related genes and lncRNAs that could be utilized as candidate markers to illustrate the molecular mechanisms underlying the growth regulation of Pacific oysters. [ABSTRACT FROM AUTHOR]

Conventional techniques to remove Fe impurities in kaolin typically involve high environmental impact and cost. Alternative methods have been focused on the use of bioleaching where Fe in kaolin is reduced with microorganisms. Early results established a noticeable effect of the bacteria on the redox state of Fe, but knowledge gaps persist such as details on the bacterial-kaolin interactions during attachment of bacteria onto kaolin surface, the metabolites produced by bacteria, and changes in Fe(II)/Fe(III) ion equilibria in solution. To bridge these gaps, this study was conducted to determine the detailed physicochemical changes in bacteria and kaolin during bioleaching through surface, structural, and chemical analysis. Bioleaching experiments were conducted for 10 days where each of the three Bacillus sp. was put in contact (at 9 × 108 CFU) with 20 g of kaolin powder using 200 mL of 10 g/L glucose solution. All samples treated with bacteria showed increasing trends in Fe(III) reduction up until day 6 or 8 followed by a slight decrease towards the end of the ten-day period. Examination of scanning electron microscope (SEM) images suggests that bacterial activity damaged the edges of kaolin particles during bioleaching. Ion chromatography (IC) results showed that during bioleaching, Bacillus sp. produced organic acids such as lactic acid, formic acid, malic acid, acetic acid, and succinic acid. EDS analysis of kaolin before and after bioleaching showed Fe removal efficiencies of up to 65.3%. Analyses of color properties of kaolin before and after bioleaching showed an improvement in whiteness index of up to 13.6%. Key points: • Dissolution of iron oxides by Bacillus species proven with phenanthroline analysis. • Organic acid type and concentration unique to species detected during bioleaching. • Whiteness index of kaolin is improved after bioleaching. [ABSTRACT FROM AUTHOR]

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae. Author summary: This article describes the discovery and characterization of multiple strains and species of viruses from the family Partitiviridae in the brewer's and baker's yeast S. cerevisiae. These novel viruses have bipartite genomes packaged in spherical viral particles with structural homology to members of the family Partitiviridae. Strikingly, yeast partitiviruses are most closely related to viruses from human pathogenic protozoa and not partitiviruses of other fungi. As partitiviruses can positively and negatively contribute to a host's physiology (including important human and plant pathogens), the presence of partitiviruses in S. cerevisiae offers a unique opportunity to study the biology of these viruses in a well-developed model system. [ABSTRACT FROM AUTHOR]

Polyphosphate (polyP) is a conserved polymer of inorganic phosphate residues that can reach thousands of moieties in length. PolyP has been implicated in cellular functions ranging from energy and phosphate homeostasis to cell signalling in eukaryotes from yeast to humans. Despite the interest in the role of polyP as a signalling molecule, the spatiotemporal regulation of polyP itself remains poorly understood. This knowledge gap limits our ability to understand how polyP impacts the physiology of normal and diseased cells and how this might be exploited in a therapeutic context. Polyphosphatases, enzymes that degrade polyP to generate shorter chains and free inorganic phosphate are ideally positioned to mediate polyP dynamics. However, little is known about how the activities of these enzymes are linked to specific cellular functions and how they might be regulated. Here, we provide an in‐depth overview of polyphosphatase enzymes in budding yeast, which has served as a workhorse for polyP research, and in mammalian cells where the enzymes that make and degrade polyP have remained elusive. We identify critical open questions in both systems and propose strategies to guide future work. [ABSTRACT FROM AUTHOR]

Background Yungui Plateau is rich in fungal diversity. Hyphomycetes, growing on submerged wood, can promote the degradation of organisms and the reuse of rotten wood energy. During an investigation of hyphomycetes in this region, 19 species of dematiaceous hyphomycetes were collected in Yungui Plateau. New information Both morphological identification and multi-gene phylogenetic analyses of ITS, tef1 and LSU sequences supported Coryneum sevenseptatis as a new species. Phaeoisaria guizhouensis and Pleurothecium yunanensis were introduced, based on morphology. Morphological descriptions and illustrations of the new species were detailed. Known species are listed with notes. [ABSTRACT FROM AUTHOR]

The biophysical properties of the cytoplasm are major determinants of key cellular processes and adaptation. Many yeasts produce dormant spores that can withstand extreme conditions. We show that spores of Saccharomyces cerevisiae exhibit extraordinary biophysical properties, including a highly viscous and acidic cytosol. These conditions alter the solubility of more than 100 proteins such as metabolic enzymes that become more soluble as spores transit to active cell proliferation upon nutrient repletion. A key regulator of this transition is the heat shock protein, Hsp42, which shows transient solubilization and phosphorylation, and is essential for the transformation of the cytoplasm during germination. Germinating spores therefore return to growth through the dissolution of protein assemblies, orchestrated in part by Hsp42 activity. The modulation of spores' molecular properties are likely key adaptive features of their exceptional survival capacities. Yeast spores are exceptionally resistant to stress due to their dormancy, but how do they exit this state? This study shows how these cells transform the biophysical properties of their cytoplasm and proteome to return to vegetative growth. [ABSTRACT FROM AUTHOR]

Background: This study aimed to isolate a novel thermotolerant bacterium that is capable of synthesizing polyhydroxyalkanoate from glycerol under high temperature conditions. Results: A newly thermotolerant polyhydroxyalkanoate (PHA) producing bacterium, Cupriavidus sp. strain CB15, was isolated from corncob compost. The potential ability to synthesize PHA was confirmed by detection of PHA synthase (phaC) gene in the genome. This strain could produce poly(3-hydroxybutyrate) [P(3HB)] with 0.95 g/L (PHA content 75.3 wt% of dry cell weight 1.24 g/L) using glycerol as a carbon source. The concentration of PHA was enhanced and optimized based on one-factor-at-a-time (OFAT) experiments and response surface methodology (RSM). The optimum conditions for growth and PHA biosynthesis were 10 g/L glycerol, 0.78 g/L NH4Cl, shaking speed at 175 rpm, temperature at 45 °C, and cultivation time at 72 h. Under the optimized conditions, PHA production was enhanced to 2.09 g/L (PHA content of 74.4 wt% and dry cell weight of 2.81 g/L), which is 2.12-fold compared with non-optimized conditions. Nuclear magnetic resonance (NMR) analysis confirmed that the extracted PHA was a homopolyester of 3-hydyoxybutyrate. Conclusion: Cupriavidus sp. strain CB15 exhibited potential for cost-effective production of PHA from glycerol. [ABSTRACT FROM AUTHOR]

Epizootic Shell Disease (ESD) has posed a great threat, both ecologically and economically, to the American lobster population of Long Island Sound since its emergence in the late 1990s. Because of the polymicrobial nature of carapace infections, causative agents for ESD remain unclear. In this study, we aimed to identify carapace microbiota associated with ESD and its potential impact on the microbiota of internal organs (green gland, hepatopancreas, intestine, and testis) using high-throughput 16S rRNA gene sequencing. We found that lobsters with ESD harbored specific carapace microbiota characterized by high abundance of Aquimarina, which was significantly different from healthy lobsters. PICRUSt analysis showed that metabolic pathways such as amino acid metabolism were enriched in the carapace microbiota of lobsters with ESD. Aquimarina, Halocynthiibacter, and Tenacibaculum were identified as core carapace bacteria associated with ESD. Particularly, Aquimarina and Halocynthiibacter were detected in the green gland, hepatopancreas, and testis of lobsters with ESD, but were absent from all internal organs tested in healthy lobsters. Hierarchical clustering analysis revealed that the carapace microbiota of lobsters with ESD was closely related to the green gland microbiota, whereas the carapace microbiota of healthy lobsters was more similar to the testis microbiota. Taken together, our findings suggest that ESD is associated with alterations in the structure and function of carapace microbiota, which may facilitate the invasion of bacteria into the green gland. [ABSTRACT FROM AUTHOR]

Background: We conducted a prospective placebo-controlled double-blind randomized Study to assess the impact of a single dose of a nutritional Supplement (AB001) on alcohol absorption in healthy subjects. Other objectives were the impact on breath alcohol content, cognitive function 1 hour after alcohol uptake and tolerability. Method: A total of 24 healthy volunteers were enrolled into the study (12 male, 12 female, age: 28.3 ± 10.8 years, BMI: 23.5 ± 5.7 kg/m²). On the experimental day, they ingested a light breakfast together with a single dose (2 capsules) of AB001 (or placebo) and drank 2 moderate glasses of spirit (a total of 0.6 g/kg body weight). Breath alcohol tests and blood draws for determination of blood alcohol levels were performed for up to 6 hours. After crossover, the experiment was repeated in the following week. Areas under the curves were calculated to determine alcohol absorption rates. Results: There was a significant reduction of blood alcohol by 10.1% (P <.001) with AB001, when compared to placebo. There was a less pronounced but also significant reduction of alcohol in the breath test by 7.2% (P <.05). No difference in the cognitive function test between AB001 and placebo could be observed 60 minutes after alcohol ingestion (22.6 ± 8.0 seconds vs 23.0 ± 11.2 seconds, n.s.). The supplement uptake was well tolerated and there were no adverse events related to the study intervention. Conclusion: Uptake of a single dose of AB001 shortly before drinking alcohol significantly reduced plasma alcohol and breath alcohol concentrations, but the effect was less pronounced compared to chronic uptake as shown previously. [ABSTRACT FROM AUTHOR]

Bacillus subtilis is a Gram-positive bacterium that is widely used in fermentation and in the pharmaceutical industry. Phage contamination occasionally occurs in various fermentation processes and causes significant economic loss. Here, we report the isolation and characterization of a temperate B. subtilis phage, termed phi18-2, from spore powder manufactured in a fermentation plant. Transmission electron microscopy showed that phi18-2 has a symmetrical polyhedral head and a long noncontractile tail. Receptor analysis showed that phi18-2 recognizes wall teichoic acid (WTA) for infection. The phage virions have a linear double-stranded DNA genome of 64,467 bp with identical direct repeat sequences of 309 bp at each end of the genome. In lysogenic cells, the phage genome was found to be present in the cytoplasm without integration into the host cell chromosome, and possibly as a linear phage-plasmid with unmodified ends. Our data may provide some insight into the molecular basis of the unique lysogenic cycle of phage phi18-2., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Fungal cell-wall-degrading enzymes have great utility in the agricultural and food industries. These cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic organisms. The existing methods used to discover these enzymes are not well adapted to fungi culture and morphology, which prevents the proper evaluation of these enzymes. We report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized droplets. The new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days (2–4 days) and could be sorted without droplet breakage. With long-term culture, we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based substrates. We also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes, such as chitinases, β-glucanases, and β-N-acetylgalactosaminidases, from a filamentous fungi droplet library that had been incubated for >4 days. The new system is portable, affordable for any laboratory, and user-friendly compared to classical droplet-based microfluidic systems. We propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells. [ABSTRACT FROM AUTHOR]

In most procedures that involve gene cloning, after the amplification of a target gene by PCR or by Real-time PCR, the purification of the trapped gene on agarose gel is a crucial stage. There are various methods for extracting genes from agarose gel by removing other contaminants. We isolated the amplified PqHMGR gene (derived from Ginseng (Panax quinquefolius)) from agarose gel by a quasi-electrophoresis device (similar to electro-elution technique). Moreover, the efficiency of this new approach was compared with that of the commercial kit 'Silica Bead DNA Gel Extraction' (Thermo Scientific American Company). Ligation to the PTG- 19 plasmid and cloning in E. coli bacteria were also done. The results showed successful isolations of targeted DNA, along with a high efficiency in producing recombinant DNA and in concluding a successful cloning procedure through this new device. The invented method provided a better purification ability than the commercial kit, but because of using the TAE 1X buffer as the purified gene storage solution, the plasmid and bacterial transformation rates were slower than the commercial kit method. It was found that using the new method for the purification of nucleotide sequences by electrophoresis and electrophoresis buffer is feasible, and that these purified fragments can be applied in cloning and sequencing. Using the TAE 1X buffer instead of distilled water did not cause problems in gene binding to PTG-19 plasmid. It also allowed a successful transformation of E. coli bacteria by the modified plasmid. Nonetheless, using TAE 1X buffer reduced the modification rate of the PTG-19 plasmid and decreased the rate of E. coli transformation by the modified plasmid. [ABSTRACT FROM AUTHOR]

This paper presents a review of the space exploration for life signature search with a special focus on the fluorescence microscope we developed for the life signature search on Mars and in other sites. Considering where, what, and how to search for life signature is essential. Life signature search exploration can be performed on the Mars surface and underground, on Venus' cloud, moon, asteroids, icy bodies (e.g., moons of Jupiter and Saturn), and so on. It is a useful strategy to consider the targeted characteristics that may be similar to those of terrestrial microorganisms, which are microorganisms with uniform spherical or rod structures with approximately 1 μm diameter surrounded by a membrane having a metabolic activity and mainly made of carbon-based molecules. These characteristics can be analyzed by using a fluorescence microscope and a combination of fluorescence pigments with specific staining characteristics to distinguish the microorganism characteristics. Section 1 introduces the space exploration for life signature search. Section 2 reviews the scientific instruments and achievements of past and ongoing Mars exploration missions closely related to astrobiology. Section 3 presents the search targets and analysis of astrobiology. Section 4 discusses the extraterrestrial life exploration methods that use a microscope together with other methods (based on mass spectrometry, morphology, detection of growth, movement, and death, etc. for microscopic and macroscopic organism). Section 5 expounds on the life signature detection fluorescence microscope, for which we have manufactured a bread board model and tested for extraterrestrial life exploration. [ABSTRACT FROM AUTHOR]

Objective: Uveal melanoma (UM) is an aggressive malignancy with a poor prognosis and no available effective treatment. Therefore, exploring a potential prognostic marker for UM could provide new possibilities for early detection, recurrence, and treatment. Methods: In this study, we used "ConsensusClusterPlus" to classify patients with UM into subgroups, screened for significant differences in immune prognostic factors between subgroups, selected three genes using LASSO (Least absolute shrinkage and selection operator) regression to construct a risk model, and performed tumor immune cell infiltration analysis on the risk model. infiltration analysis, and then verified the heterogeneous role of the 3 core genes in other cancers by pan-cancer analysis and validate its expression by RT-qPCR in normal and tumor cells. Results: We consistently categorized 80 UM patients into two subgroups after the immunogenetic set, where the UM1 subgroup had a better prognosis than the UM2 subgroup, and used 3 immune-related genes AZGP1, SLCO5A1, and CTF1 to derive risk scores as independent prognostic markers and predictors of UM clinicopathological features. We found significant differences in overall survival (OS) between low- and high-risk groups, and prognostic models were negatively correlated with B cell and myeloid dendritic cell and positively correlated with CD8+ T cell AZGP1 and CTF1 were significantly upregulated in UM cells compared with normal UM cells. Conclusion: Immunogens are significantly associated with the prognosis of UM, and further classification based on genetic characteristics may help to develop immunotherapeutic strategies and provide new approaches to develop customized treatment strategies for patients. [ABSTRACT FROM AUTHOR]

The contamination of environmental sully with antibiotics is regarded as a major problem today and predictable to attain more recognition in near future. However, human intervention resulting in antibiotic consumption is being enhancing all around the world. Our review of literature revealed the role of microbiome in sully and how antibiotic resistant genes raised. The structure of antibiotics basically influenced by natural components such as biotic and abiotic push which shifts based on different soils. Therefore, management of microbiome in soil and their expression studies were distinctively revealed. The assessment of antibiotic resistance genes with help of next generation sequencing provided a clear comprehension on genome and transcriptome of the bacterial genes. Thus, interaction of microbiome with soil can also be well understood. The current findings in our study will guide every researcher to follow logical protocol in analyzing microbiota composition is covered as well and also to understand its metagenomic and sequenced with next-generation sequencer which helps to comprehend the diverse micro-flora present in soil and its operation. Finally, later progresses in bioinformatics computer program, flow of work, and applications for analyzing metagenomic information are put in a nutshell. [ABSTRACT FROM AUTHOR]

Aquaculture is a critical food source for the world's growing population, producing 52% of the aquatic animal products consumed. Marine aquaculture (mariculture) generates 37.5% of this production and 97% of the world's seaweed harvest. Mariculture products may offer a climate-friendly, high-protein food source, because they often have lower greenhouse gas (GHG) emission footprints than do the equivalent products farmed on land. However, sustainable intensification of low-emissions mariculture is key to maintaining a low GHG footprint as production scales up to meet future demand. We examine the major GHG sources and carbon sinks associated with fed finfish, macroalgae and bivalve mariculture, and the factors influencing variability across sectors. We highlight knowledge gaps and provide recommendations for GHG emissions reductions and carbon storage, including accounting for interactions between mariculture operations and surrounding marine ecosystems. By linking the provision of maricultured products to GHG abatement opportunities, we can advance climate-friendly practices that generate sustainable environmental, social, and economic outcomes. [ABSTRACT FROM AUTHOR]

Secreted acid phosphatases (APases) dephosphorylate extracellular organic phosphate compounds to supply inorganic phosphate (Pi) to maintain cellular functions. Here, we show that APases are necessary to maintain a normal replicative lifespan in Saccharomyces cerevisiae. Deletion of all four APase genes shortened the lifespan in yeast strains on synthetic media (irrespective of the concentrations of Pi in the media), but it did not affect the intracellular ortho‐ and polyphosphate levels. Deletion of inositol‐pentakisphosphate 2‐kinase (IPK1), which encodes inositol‐pentakisphosphate 2‐kinase, restored the lifespan in APase‐null mutants, and IPK1 overexpression shortened the lifespan in wild‐type strains. Overexpression of inositol hexakisphosphate (IP6) and heptakisphosphate kinases, KCS1 and VIP1, recovered the lifespan in APase‐null mutants. Thus, yeast APases modulate the replicative lifespan, probably through dephosphorylation of intracellular IP6. [ABSTRACT FROM AUTHOR]

In most eukaryotic genomes, tandemly repeated copies of 5S rRNA genes are clustered outside the nucleolus organizer region (NOR), which normally encodes three other major rRNAs: 18S, 5.8S, and 28S. Our analysis of turtle rDNA sequences has revealed a 5S rDNA insertion into the NOR intergenic spacer in antisense orientation. The insertion (hereafter called NOR-5S rRNA gene) has a length of 119 bp and coexists with the canonical 5S rDNA clusters outside the NOR. Despite the ∼20% nucleotide difference between the two 5S gene sequences, their internal control regions for RNA polymerase III are similar. Using the turtle Trachemys scripta as a model species, we showed the NOR-5S rDNA specific expression in oocytes. This expression is concurrent with the NOR rDNA amplification during oocyte growth. We show that in vitellogenic oocytes, the NOR-5S rRNA prevails over the canonical 5S rRNA in the ribosomes, suggesting a role of modified ribosomes in oocyte-specific translation. The orders Testudines and Crocodilia seem to be the only taxa of vertebrates with such a peculiar rDNA organization. We speculate that the amplification of the 5S rRNA genes as a part of the NOR DNA during oogenesis provides a dosage balance between transcription of all the four ribosomal RNAs while producing a maternal pool of extra ribosomes. We further hypothesize that the NOR-5S rDNA insertion appeared in the Archelosauria clade during the Permian period and was lost later in the ancestors of Aves. [ABSTRACT FROM AUTHOR]

The Gram positive bacterium Bacillus subtilis and its relatives are capable of forming a durable dormant long-lasting spore. Although spores can remain dormant for years, they possess the remarkable capacity to rapidly resume life and convert into actively growing cells. This cellular transition initiates with a most enigmatic irreversible event, termed germination, lasting only for a few minutes. Germination is typified by a morphological conversion that culminates in loss of spore resilient properties. Yet, the molecular events occurring during this brief critical phase are largely unknown. The current widely accepted view considers germination to occur without the need for any macromolecule synthesis; however, accumulating data from our laboratory and others, highlighted here, provide evidence that both transcription and translation occur during germination and are required for its execution. We further underline numerous overlooked studies, conducted mainly during the 1960s–1970s, reinforcing this notion. We propose to revisit the fascinating process of spore germination and redefine it as a pathway involving macromolecule synthesis. We expect our perspective to shed new light on the awakening process of a variety of spore-forming environmental, commensal, and pathogenic bacteria and possibly be applicable to additional organisms displaying a quiescent life form. In this review, we synthesize old and current data to evoke that, in contrast to current dogma, bacterial spore germination demands macromolecule synthesis. [ABSTRACT FROM AUTHOR]

We examined the effect of interacting dipicolinic acid and its calcium chelate on the wet and dry density of DNA. Complexes are produced whose densities are different from those of the individual components. Also, we observed two modes of binding, one strong the other weak, between DPA or CaDPA and DNA. The strength of the binding modes was reflected in the rate of dissolution of the complexes as monitored by changes in wet density with time and temperature. We conclude from these and other data in the literature that the interaction of dipicolinic acid with DNA not only influences the spore wet density and the ratio of core/core cortex volume, but may also influence the spore heat resistance. [ABSTRACT FROM AUTHOR]

A low-affinity and a high-affinity sylose proton symport operated simultaneously in both starved and non-starved cells of Pichia stipitis. Glucose competed with xylose for transport by the low-affinity system and inhibited xylose transport by the high-affinity system non-competitively. The low affinity system was subject to substrate inhibition when glucose but not when xylose was the substrate. The differences between the characteristics of monosaccharide transport by Pichia stipitis and its imperfect state, Candida shehatae, are discussed. [ABSTRACT FROM AUTHOR]

Phages are viruses of bacteria and are the smallest and most common biological entities in the environment. They can reproduce immediately after infection or integrate as a prophage into their host genome. SPβ is a prophage of the Gram-positive model organism Bacillus subtilis 168, and it has been known for more than 50 years. It is sensitive to dsDNA damage and is induced through exposure to mitomycin C or UV radiation. When induced from the prophage, SPβ requires 90 min to produce and release about 30 virions. Genomes of sequenced related strains range between 128 and 140 kb, and particle-packed dsDNA exhibits terminal redundancy. Formed particles are of the Siphoviridae morphotype. Related isolates are known to infect other B.subtilis clade members. When infecting a new host, SPβ presumably follows a two-step strategy, adsorbing primarily to teichoic acid and secondarily to a yet unknown factor. Once in the host, SPβ-related phages pass through complex lysis–lysogeny decisions and either enter a lytic cycle or integrate as a dormant prophage. As prophages, SPβ-related phages integrate at the host chromosome's replication terminus, and frequently into the spsM or kamA gene. As a prophage, it imparts additional properties to its host via phage-encoded proteins. The most notable of these functional proteins is sublancin 168, which is used as a molecular weapon by the host and ensures prophage maintenance. In this review, we summarise the existing knowledge about the biology of the phage regarding its life cycle and discuss its potential as a research object. [ABSTRACT FROM AUTHOR]

The occurrence of Precambrian stromatolites is closely related to the ancient seawater composition and the evolution of life. It is also a potential oil and gas reservoir. In what kind of environment the stromatolites of the upper Ediacaran Qigebulak Formation in the Tarim Basin developed, and whether they constitute potential hydrocarbon reservoirs, remained unclear. Stromatolites occur in 1–5 m thick layers, interbedded with thrombolites and dolostones. Distinct stromatolite morphologies were observed, including columnar, sinuous, short columnar, domal, and conical shapes. The δ13C values of the stromatolites (6.1‰ on average) are slightly lighter than those of the dolostones, and the δ18O values (− 1.4‰ on average) are significantly heavier than that of the dolostones. The stromatolites have a relatively high content of rare-earth elements and a minor Ce anomaly. The geochemical results imply that the stromatolites formed in an evaporative hypersaline lagoon environment. The presence of barrier dams near the coast led to the formation of lagoons, where hypersalinity was achieved when evaporation was greater than marine or freshwater input. High salinity conditions inhibited the growth of Ediacaran metazoans, allowing the buildup of stromatolites in the restricted lagoons. The stromatolites are rich in primary fenestral pores and sheet-like cavities along the laminae, and the secondary dissolution pores and vugs are related to meteoric karstification. The stromatolites, together with dolostones and thrombolites, constitute the majority of the hydrocarbon reservoirs in the Upper Ediacaran in the Tarim Basin. The results clarify the environment where the stromatolites could still flourish and be well preserved whereas they significantly declined globally throughout the Neoproterozoic elsewhere. The results imply that extensive stromatolites in the Proterozoic strata are potentially important reservoir rocks of Precambrian petroleum systems. [ABSTRACT FROM AUTHOR]

Apart from actual incubation and/or testing, the mandated way to determine the microbial safety of thermally preserved foods is still anchored in the premise that the isothermal inactivation of bacterial cells and spore survival follows first-order kinetics. This is despite growing evidence to the contrary, and that the D value's temperature-dependence too need not follow the log-linear model. Also, for technical reasons, the experimental detection level of survival ratios is usually four to six orders of magnitudes higher than that expected to assure a safe product. The theoretical implications of such a gap combined with non-linear inactivation kinetics are explored through simulations with especially constructed mathematical survival models. One of these models produces apparently log-linear or Weibullian survival patterns above the detection despite having a definite thermal death time, while the other has a substantial asymptotic residual survival level albeit below the detection level. The simulations highlight the notion that there is not enough information in an experimental survival curve's shape to allow its continuation to below the detection level. Thus any thermal death time determined by extrapolation has no logical basis and can lead to either underestimation or overestimation of the thermal process's lethality depending on the model chosen to describe it. The analysis lends support to the notion that safety factors and efficacy criteria in thermal processes should be based on observable survival ratios and not on log-linear kinetics. [ABSTRACT FROM AUTHOR]

The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and reaches hundreds by the lampbrush chromosome stage (pre-vitellogenesis). RNA-polymerase I, fibrillarin, and PCNA immunodetection in the amplified nucleoli and FISH of the 5'ETS probe to the oocyte nuclear content suggest pre-rRNA and rDNA synthesis in the nucleoli at all stages studied. This implies a continuous reproduction of the nucleoli during oocyte development from early diplotene up to vitellogenesis. The data obtained offer a different way for rDNA amplification and formation of extrachromosomal nucleoli in turtle oocytes compared with the amplified nucleoli formation in amphibian and fish oocytes. In the Sauropsida clade of Archelosauria, which includes turtles, crocodiles, and birds, rDNA function is known to be suppressed in avian oogenesis during the lampbrush stage (Gaginskaya et al. in Cytogenet Genome Res 124:251–267, 2009). [ABSTRACT FROM AUTHOR]

Bacillus anthracis, a spore-forming gram-positive bacterium, causes anthrax. The external surface of the exosporium is coated with glycosylated proteins. The sugar additions are capped with the unique monosaccharide anthrose. The West African Group (WAG) B. anthracis have mutations rendering them anthrose deficient. Through genome sequencing, we identified 2 different large chromosomal deletions within the anthrose biosynthetic operon of B. anthracis strains from Chile and Poland. In silico analysis identified an anthrose-deficient strain in the anthrax outbreak among European heroin users. Anthrose-deficient strains are no longer restricted to West Africa so the role of anthrose in physiology and pathogenesis was investigated in B. anthracis Sterne. Loss of anthrose delayed spore germination and enhanced sporulation. Spores without anthrose were phagocytized at higher rates than spores with anthrose, indicating that anthrose may serve an antiphagocytic function on the spore surface. The anthrose mutant had half the LD50 and decreased time to death (TTD) of wild type and complement B. anthracis Sterne in the A/J mouse model. Following infection, anthrose mutant bacteria were more abundant in the spleen, indicating enhanced dissemination of Sterne anthrose mutant. At low sample sizes in the A/J mouse model, the mortality of ΔantC-infected mice challenged by intranasal or subcutaneous routes was 20% greater than wild type. Competitive index (CI) studies indicated that spores without anthrose disseminated to organs more extensively than a complemented mutant. Death process modeling using mouse mortality dynamics suggested that larger sample sizes would lead to significantly higher deaths in anthrose-negative infected animals. The model was tested by infecting Galleria mellonella with spores and confirmed the anthrose mutant was significantly more lethal. Vaccination studies in the A/J mouse model showed that the human vaccine protected against high-dose challenges of the nonencapsulated Sterne-based anthrose mutant. This work begins to identify the physiologic and pathogenic consequences of convergent anthrose mutations in B. anthracis. A study of the spontaneous loss of the spore coat monosaccharide anthrose suggests that convergent evolution in several anthrax strains towards increased pathogenicity could exacerbate global human and animal anthrax disease. [ABSTRACT FROM AUTHOR]