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The mystery of the third Lucretia
While traveling in London, Paris, and Amsterdam, fourteen-year-old best friends Kari and Lucas solve an international art forgery mystery.
Book
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene \"inventions\" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
Journal Article
Shades within us : tales of migrations and fractured borders
\"Migration comes in unlimited shades of colour where we straddle between physical, emotional, and spiritual boundaries within ourselves-and within our worlds and beyond...Who are the shades within us? We are called immigrants, locals, explorers, natives, settlers, pioneers, discoverers, newcomers, drifters, tenants, transients, nomads, expatriates, wanderers, evacuees, refugees, pilgrims, aliens, foreigners, squatters, visitors, intruders, conquerors, asylum seekers, urbanites, outsiders ... Take a journey with twenty-one speculative fiction authors through fractured borders and open frontiers, and break the monolith of our assumptions about migrants and \"others.\" Stories that transcend borders, generations, and culture-always captivating and relatable. In the end, we get a glimpse into our human need in face of change-realized or lost-to hold fast to home, tradition, family, and the places in which we find them. And no matter how difficult or challenging lives can be-the human spirit will triumph in the end as all emotions are universal: we born, we dream, we strive, we die. Introduction by Eric Choi and Gillian Clinton. In addition to dealing with migrations, immigrants, and anti-discrimination, the book also deals with mental health and mental illness. There is an appendix in the book for Mental Health Resources and another appendix for Anti-Discrimination Resources.\"-- Provided by publisher.
Book
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Choice genomes sequenced
The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach has been taken in the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, which advocates choosing genomes based on the organism's phylogenetic position, with the aim filling in the gaps in sequencing along on bacterial and archaeal branches of the tree of life. The value of this approach has been demonstrated by a pilot study of the genome sequences of 56 culturable species selected to maximize phylogenetic coverage. Analysis of the sequences provides insights into phylogenetics, protein function and genome annotation.
There are now nearly 1,000 completed bacterial and archaeal genomes available, but as most of them were chosen for sequencing on the basis of their physiology, the data are limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, the genomes of 56 species of Bacteria and Archaea selected to maximize phylogenetic coverage are now sequenced and analysed.
Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms
1
. There are now nearly 1,000 completed bacterial and archaeal genomes available
2
, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution
3
,
4
,
5
. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
Journal Article
Thinkterior : amazing bespoke kids interiors
\"This book showcases indoor and outdoor spaces created by Thinkterior, a design firm devoted to designing, fabricating and installing environments for children.\"--Provided by publisher.
Book
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
Background
Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus,
Phanerochaete carnosa
, has been isolated almost exclusively from softwoods, while most other known white-rot species, including
Phanerochaete chrysosporium
, were mainly isolated from hardwoods. Accordingly, it is anticipated that
P. carnosa
encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the
P. carnosa
genome sequence and its comparative analysis with the previously reported
P. chrysosporium
genome.
Results
P. carnosa
encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that
P. carnosa
is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably,
P. carnosa
possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of
P. chrysosporium
. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of
P. carnosa
to various substrates including coniferous heartwood.
Conclusions
The
P. carnosa
genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in
P. carnosa
, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.
Journal Article
Clinicians’ perspective of picture archiving and communication systems at Charlotte Maxeke Johannesburg Academic Hospital
BackgroundPicture archiving and communication systems (PACS) are now an established means of capturing, storing, distribution and viewing of all radiology images. The study was conducted in a quaternary hospital, Charlotte Maxeke Johannesburg Academic Hospital (CMJAH), part of the University of the Witwatersrand teaching circuit, in South Africa.ObjectivesTo measure the clinicians’ perceived benefits and challenges of PACS. To document perceived views on how the current PACS can be improved.MethodThis was a cross-sectional observational study over a period of 5 months from September 2021 to January 2022 carried out at CMJAH. Questionnaires were distributed to referring clinicians with PACS experience. Descriptive statistics was conducted. Categorical variables were presented as frequency and percentages. The continuous variables were presented as means ± standard deviation.ResultsA survey with a response rate of 54% found the benefits most reported by clinicians were improved patient care, less time needed to review an exam, improved image comparison and consultation efficiency. With respect to perceived challenges, the unavailability of images at the bedside, problems with access and the lack of advanced image manipulating software were noted. The most frequent recommendations on improvements focused on the aforementioned challenges.ConclusionHospital-wide PACS was viewed beneficial by most clinicians. Nonetheless, there are a few aspects that deserve attention to improve the functionality and access of the system.ContributionThe findings will assist in future hospital or provincial-wide PACS deployment projects.
Journal Article
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics
Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.
Journal Article
The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader
Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.
Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of \"specialized\" plasmids.
The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.
Journal Article
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production
Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.
Journal Article