Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterising cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialised compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterised. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and heme, is incomplete. We discuss tools that may aid characterisation of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterisation of individual proteins

Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria.

Breast milk enhances the predominance of Bifidobacterium species in the infant gut, probably due to its large concentration of human milk oligosaccharides (HMO). Here we screened infant-gut isolates of Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum using individual HMO, and compared the global transcriptomes of representative isolates on major HMO by RNA-seq. While B. infantis displayed homogeneous HMO-utilization patterns, B. bifidum were more diverse and some strains did not use fucosyllactose (FL) or sialyllactose (SL). Transcriptomes of B. bifidum SC555 and B. infantis ATCC 15697 showed that utilization of pooled HMO is similar to neutral HMO, while transcriptomes for growth on FL were more similar to lactose than HMO in B. bifidum. Genes linked to HMO-utilization were upregulated by neutral HMO and SL, but not by FL in both species. In contrast, FL induced the expression of alternative gene clusters in B. infantis. Results also suggest that B. bifidum SC555 does not utilize fucose or sialic acid from HMO. Surprisingly, expression of orthologous genes differed between both bifidobacteria even when grown on identical substrates. This study highlights two major strategies found in Bifidobacterium species to process HMO, and presents detailed information on the close relationship between HMO and infant-gut bifidobacteria

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans.

UnlabelledMany symbiotic gut bacteria possess the ability to degrade multiple polysaccharides, thereby providing nutritional advantages to their hosts. Like microorganisms adapted to other complex nutrient environments, gut symbionts give different metabolic priorities to substrates present in mixtures. We investigated the responses of Bacteroides thetaiotaomicron, a common human intestinal bacterium that metabolizes more than a dozen different polysaccharides, including the O-linked glycans that are abundant in secreted mucin. Experiments in which mucin glycans were presented simultaneously with other carbohydrates show that degradation of these host carbohydrates is consistently repressed in the presence of alternative substrates, even by B. thetaiotaomicron previously acclimated to growth in pure mucin glycans. Experiments with media containing systematically varied carbohydrate cues and genetic mutants reveal that transcriptional repression of genes involved in mucin glycan metabolism is imposed by simple sugars and, in one example that was tested, is mediated through a small intergenic region in a transcript-autonomous fashion. Repression of mucin glycan-responsive gene clusters in two other human gut bacteria, Bacteroides massiliensis and Bacteroides fragilis, exhibited variable and sometimes reciprocal responses compared to those of B. thetaiotaomicron, revealing that these symbionts vary in their preference for mucin glycans and that these differences occur at the level of controlling individual gene clusters. Our results reveal that sensing and metabolic triaging of glycans are complex processes that vary among species, underscoring the idea that these phenomena are likely to be hidden drivers of microbiota community dynamics and may dictate which microorganisms preferentially commit to various niches in a constantly changing nutritional environment.ImportanceHuman intestinal microorganisms impact many aspects of health and disease, including digestion and the propensity to develop disorders such as inflammation and colon cancer. Complex carbohydrates are a major component of the intestinal habitat, and numerous species have evolved and refined strategies to compete for these coveted nutrients. Our findings reveal that individual bacteria exhibit different preferences for carbohydrates emanating from host diet and mucosal secretions and that some of these prioritization strategies are opposite to one another. Thus, we reveal new aspects of how individual bacteria, some with otherwise similar metabolic potential, partition to "preferred niches" in the complex gut ecosystem, which has important and immediate implications for understanding and predicting the behavioral dynamics of this community

Proteomic analysis of Bifidobacterium longum subsp. infantis reveals the metabolic insight on consumption of prebiotics and host glycans.

Bifidobacterium longum subsp. infantis is a common member of the intestinal microbiota in breast-fed infants and capable of metabolizing human milk oligosaccharides (HMO). To investigate the bacterial response to different prebiotics, we analyzed both cell wall associated and whole cell proteins in B. infantis. Proteins were identified by LC-MS/MS followed by comparative proteomics to deduce the protein localization within the cell. Enzymes involved in the metabolism of lactose, glucose, galactooligosaccharides, fructooligosaccharides and HMO were constitutively expressed exhibiting less than two-fold change regardless of the sugar used. In contrast, enzymes in N-Acetylglucosamine and sucrose catabolism were induced by HMO and fructans, respectively. Galactose-metabolizing enzymes phosphoglucomutase, UDP-glucose 4-epimerase and UTP glucose-1-P uridylytransferase were expressed constitutively, while galactokinase and galactose-1-phosphate uridylyltransferase, increased their expression three fold when HMO and lactose were used as substrates for cell growth. Cell wall-associated proteomics also revealed ATP-dependent sugar transport systems associated with consumption of different prebiotics. In addition, the expression of 16 glycosyl hydrolases revealed the complete metabolic route for each substrate. Mucin, which possesses O-glycans that are structurally similar to HMO did not induced the expression of transport proteins, hydrolysis or sugar metabolic pathway indicating B. infantis do not utilize these glycoconjugates

Archaeology of Atafu, Tokelau: Some initial results from 2008

Surface survey, shovel testing, and stratigraphic excavations were done on Atafu Atoll in Tokelau during August 2008. Initial results suggest that Fale Islet has the most potential for further archaeological research. Dense cultural deposits on this islet are >1 m (39 in.) deep. Cultural material recovered includes food bone, fire-affected volcanic rock, tool-grade basalt flakes and tool fragments, Tridacna shell adzes, and pearl-shell fishhook fragments. Dog bone occurs from the earliest deposits through to the late prehistoric, while pig bone is found only in historic contexts. Fish bone is common throughout, and, with the exception of Tridacna, there are few edible mollusk remains. Initial EDXRF (Energy Dispersive X-Ray Fluorescence) analyses have found the basalt to be consistent with documented sources on Tutuila, Samoa. Basal radiocarbon dates from two excavation units are 660-540 cal. BP and 500-310 cal. BP (at 2σ)

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content.

Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis

Advancing time- and angle-resolved photoemission spectroscopy: The role of ultrafast laser development

In the last decade, there has been a proliferation of laser sources for time- and angle-resolved photoemission spectroscopy (TR-ARPES), building on the proven capability of this technique to tackle important scientific questions. In this review, we aim to identify the key motivations and technologies that spurred the development of various laser sources, from frequency up-conversion in nonlinear crystals to high-harmonic generation in gases. We begin with a historical overview of the field in Sec.1, framed by advancements in light source and electron spectrometer technology. An introduction to the fundamental aspects of the photoemission process and the observables that can be studied is given in Sec.2, along with its dependencies on the pump and probe pulse parameters. The technical aspects of TR-ARPES are discussed in Sec.3. Here, experimental limitations such as space charge and resultant trade-offs in source parameters are discussed. Details of various systems and their approach to these trade-offs are given in Sec.4. Within this discussion, we present a survey of TR-ARPES laser sources; a meta-analysis of these source parameters showcases the advancements and trends in modern systems. Lastly, we conclude with a brief discussion of future directions for TR-ARPES and its capabilities in elucidating equilibrium and non-equilibrium observables, as well as its integration with micro-ARPES and spin-resolved ARPES (Sec.5).Comment: 104 pages, 27 figure

Examining Intervening Variables Of The EC Consumer Behavior Model: The Powersellertm And Phenomenon Search Products

The EC consumer behavioral model is an effort to describe the electronic commerce environment, which includes electronic auctions. The model identifies intervening variables that are related to vendors such as trustworthiness (merchant characteristic) and product brand and availability (product characteristics).  In this paper, we have attempted to explore PowerSellersTM, a specific intermediary characteristic for electronic auctions.  Specifically, we analyzed PowerSellersTM on products with limited availability and high demand.  Linear regression models were used to analyze the intermediary characteristics and purchase price.   Findings support the possibility that phenomenon search products attenuate the impact of a seller’s rating on auctions prices. This paper serves as a specific investigation to better understand consumer online purchase intensions within the EC consumer behavior model

IS Programs Responding to Industry Demands for Data Scientists: A Comparison Between 2011-2016

The term data scientist has only been in common use since 2008, but in 2016 it is considered one of the top careers in the United States. The purpose of this paper is to explore the growth of data science content areas such as analytics, business intelligence, and big data in AACSB Information Systems (IS) programs between 2011 and 2016. A secondary purpose is to analyze the effect of IS programs’ adherence to IS 2010 Model Curriculum Guidelines for undergraduate MIS programs, as well as the impact of IS programs offering an advanced database course in 2011 on data science course offerings in 2016. A majority (60%) of AACSB IS programs added data science-related courses between 2011 and 2016. Results indicate dramatic increases in courses offered in big data analytics (583%), visualization (300%), business data analysis (260%), and business intelligence (236%). ANOVA results also find a significant effect of departments offering advanced database courses in 2011 on new analytics course offerings in 2016. A Chi-Square analysis did not find an effect of IS 2010 Model Curriculum adherence on analytics course offerings in 2016. Implications of our findings for an MIS department’s ability to respond to changing needs of the marketplace and its students are discussed