Full plastomes have recently proven to be a valuable data source for resolving recalcitrant phylogenetic relationships in the flowering plant family Bromeliaceae. The study of complete plastomes has ...additionally led to the discovery of new structural rearrangements and advanced our understanding of bromeliad plastome diversity and evolution. Here, we focus on the study of full plastomes of the bromeliad subfamily Hechtioideae to assess phylogenetic relationships, marker informativeness, and plastome structure and evolution. Using whole‐genome sequencing data, we de novo assembled and annotated new plastid genomes of 19 Hechtioideae species plus one representative each from the Pitcairnioideae and Puyoideae subfamilies and compared them with four additional available plastomes from other bromeliad subfamilies. Our phylogenetic analysis using complete plastome sequences not only recovered the three currently recognized genera of Hechtioideae as monophyletic, strongly supporting Mesoamerantha as sister of Bakerantha and Hechtia, but also improved statistical support at different phylogenetic depths within the subfamily. We identified a set of highly informative loci, some of them explored for the first time in Hechtioideae. Structural rearrangements, including expansions and contractions of the inverted repeats, large inversions, and gene loss and potential pseudogenization were detected mainly within the genus Hechtia. Evolutionary trait rate shifts were associated with the size and guanine–cytosine content of the small single copy and inverted repeats.
Analysis of complete plastome sequences obtained by whole‐genome sequencing improved statistical support across different phylogenetic depths in Hechtioideae and allowed the identification of highly informative loci previously unexplored in this lineage. Our plastome comparative analysis allowed us to identify several structural rearrangements in the subfamily, including expansions and contractions of the inverted repeat, large inversions, gene loss, and potential pseudogenization. Evolutionary trait rate shifts were detected at different Hechtioideae lineages in the size and guanine–cytosine content of the small single copy and inverted repeats.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast ...amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e.,
Guzmania
,
Tillandsia
, and
Vriesea
) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits’ rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.
Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages ...of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse
subgenus
(Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.
Abstract
We present the complete mitochondrial genome of Tzotzilthelphusa villarosalensisVillalobos & Álvarez, 2013, a freshwater crab from Mexico. This is the first mitochondrial genome reported for ...the superfamily Pseudothelphusoidea. We performed a de novo assembly from genome skimming reads. The mitochondrial genome of T. villarosalensis has a length of 17,203 bp and its gene topology is similar to other freshwater and marine families, e.g., the position of the cytochrome oxidase complex subunits and ATA synthetase, even the order of nad3, nad5, nad4, nad4L, nad6, and cytb. By contrast, the order and organization of genes like the 16S, 12S, and nad1 are different depending on the phylogenetic group with which they are compared. The phylogenetic analyses placed T. villarosalensis as a sister group of all freshwater crabs reported until now and as part of the subsection Heterotremata. This complete mitochondrial genome could be a reference for further genomic studies of the family Pseudothelphusidae and other primary freshwater crabs.
Close contact between cats and humans increases the risk of transmission of zoonotic pathogens, through bites and scratches due to the complexity of microorganisms in the oral and nail microbiotas of ...felines. This study investigated the presence of bacteria and fungi in the oral cavity and claws of 100 apparently healthy cats using conventional and selective microbiological culture media, and next-generation sequencing (NGS) and mass spectrometry (MALDI-TOF MS). Furthermore, antimicrobial susceptibility testing of bacteria isolates was performed by disc diffusion method. In total, 671 bacteria and 33 yeasts were identified by MALDI-TOF MS. Neisseria animaloris (10.8 %), Staphylococcus felis (8.5 %), and Pasteurella multocida (7 %) were the most prevalent bacteria in oral cavity samples (n = 343), while the most common yeast (n = 19) was Candida albicans (68.4 %). Staphylococcus pettenkoferi (13.4 %), Staphylococcus felis (6.4 %), and Staphylococcus simulans (5.8 %) were the prevalent bacteria identified in the claw samples (n = 328), while Rhodotorula mucilaginosa (57.2 %) was the most common yeast (n = 14). NGS predominantly identified the genera Moraxella, Neisseria, Pasteurella, and Fusobacterium in oral cavity samples, whereas enterobacteria and staphylococci were prevalent in nail bed samples. In addition, the genera Capnocytophaga and Bartonella were identified, which have been described in serious human infections secondary to feline aggressions. Levofloxacin, marbofloxacin, and amoxicillin/clavulanic acid were the most effective drugs against the main groups of bacteria identified. Multidrug resistance was observed in 17 % of the bacterial isolates. Furthermore, three staphylococci harboring the methicillin resistance gene mecA were identified. We highlight the complexity of microorganisms inhabiting the oral/claw microbiotas of cats, the high resistance rate of the isolates to conventional antimicrobial agents, and the zoonotic risk of aggressions caused by bites and scratches from domestic cats.
•A combination of techniques was used to assess oral and claw microbiota of cats.•First time NGS was used to describe the claw microbiota of healthy cats.•First time NGS was used to describe the oral microbiota of healthy cats in Brazil.•Pathogenic and zoonotic bacteria were identified in the microbiota of healthy cats.•NGS revealed great complexity of unculturable microorganisms.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
A multistep and diversity‐oriented synthetic route aiming at the A3 coupling/domino cyclization of o‐ethynyl anilines, aldehydes and s‐amines is described. The preparation of the corresponding ...precursors included a series of transformations, such as haloperoxidation and Sonogashira cross‐coupling reactions, amine protection, desilylation and amine reduction. Some products of the multicomponent reaction underwent further detosylation and Suzuki coupling. The resulting library of structurally diverse compounds was evaluated against blood and liver stage malaria parasites, which revealed a promising lead with sub‐micromolar activity against intra‐erythrocytic forms of Plasmodium falciparum. The results from this hit‐to‐lead optimization are hereby reported for the first time.
A structurally diverse library of indoles was prepared using a straightforward procedure, where a multicomponent reaction was explored to introduce chemical diversity at a reduced number of synthetic steps. From this underexplored scaffold emerged a potent indole lead with unprecedented antimalarial activity against blood‐stage malaria parasites.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
This phase III study examined efficacy of the synthetic Toll-like receptor 9-activating oligodeoxynucleotide PF-3512676 in combination with standard paclitaxel/carboplatin chemotherapy in patients ...with advanced non-small-cell lung cancer (NSCLC).
Chemotherapy-naive patients with stage IIIB or IV NSCLC were randomly assigned (1:1) to receive up to six courses of paclitaxel/carboplatin (intravenous paclitaxel 200 mg/m(2) and carboplatin at area under the concentration-time curve 6 on day 1 of a 3-week cycle) alone (control arm) or in combination with 0.2 mg/kg subcutaneous PF-3512676 on days 8 and 15 (investigational arm). Primary end point was overall survival (OS).
Baseline demographics were similar across arms (N = 828). Most patients (88%) had stage IV disease. Median OS and median progression-free survival (PFS) were similar (OS: investigational arm, 10.0 months v control arm, 9.8 months; P = .56; PFS: investigational arm, 4.8 months v control arm, 4.7 months; P = .79). Most commonly reported PF-3512676-related adverse events (AEs) were mild-to-moderate local injection site reactions, pyrexia, and flu-like symptoms. In the investigational arm, grades 3 to 4 AEs, including neutropenia, thrombocytopenia, and anemia, were more frequent, and more patients had one or more sepsis-related AEs versus controls (17 v 3). At first interim analysis, the Data Safety Monitoring Committee recommended study discontinuation because of lack of incremental efficacy and more sepsis-related serious AEs in the PF-3512676 arm. Administration of PF-3512676, but not chemotherapy, was halted.
Addition of PF-3512676 to paclitaxel/carboplatin did not improve OS or PFS versus paclitaxel/carboplatin alone for first-line treatment of patients with advanced NSCLC but did increase toxicity. This regimen cannot be recommended for treating patients with advanced NSCLC.
The Front Cover depicts a female Anopheles spp. mosquito, the vector of Plasmodium falciparum and perhaps the most iconic image associated with the fight against malaria, which inspects the structure ...of a new indole scaffold with promising activity against blood‐stage malaria parasites, under the moonlight (the vector has a nocturnal feeding habit, where transmission occurs). The highlighted lead compound is rising to the moon and above blood‐stage parasitic forms of P. falciparum, in which this new scaffold revealed preferential inhibitory activity. The copyrighted Anopheles picture is used with the permission of Prof. Laurence J. Zwiebel. Cover design by Natália Marques Mota. More information can be found in the Research Article by Gustavo da Silva, Rui Moreira et al.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Abstract
A multistep and diversity‐oriented synthetic route aiming at the A
3
coupling/domino cyclization of
o
‐ethynyl anilines, aldehydes and
s
‐amines is described. The preparation of the ...corresponding precursors included a series of transformations, such as haloperoxidation and Sonogashira cross‐coupling reactions, amine protection, desilylation and amine reduction. Some products of the multicomponent reaction underwent further detosylation and Suzuki coupling. The resulting library of structurally diverse compounds was evaluated against blood and liver stage malaria parasites, which revealed a promising lead with sub‐micromolar activity against intra‐erythrocytic forms of
Plasmodium falciparum
. The results from this hit‐to‐lead optimization are hereby reported for the first time.
Full text
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
