$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples

Several of the biggest challenges in taxonomy and systematics are related to a toxic mixture of small size, abundance, and rarity. There are too many species in groups with too few taxonomists and many of these species are very rare and hard to find because they are hidden in mass samples. To make matters worse, these species often have life‐history stages that are morphologically so different that it is difficult to identify them as semaphoronts of the same species. We demonstrate that these biodiversity challenges can be addressed with cost‐effective molecular markers. Here, we describe a next‐generation‐sequencing protocol that can yield barcodes at a chemical cost of < 0.40 USD per specimen. We use this protocol to generate molecular markers for 1015 specimens of tropical midges (Diptera: Chironomidae). The barcodes cluster into 52–61 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering (OC), Generalized Mixed Yule Coalescent (GMYC), or Poisson Tree Process (PTP) is used. More than half of the putative species are rare (< 10 specimens) and we are able to match larvae and adults for 24 of these OTUs. We argue that the proposed protocol will help with processing specimen‐rich biodiversity samples at low cost.     

Cinnamaldehydes inhibit thioredoxin reductase and induce Nrf2: potential candidates for cancer therapy and chemoprevention

Trans-cinnamaldehyde (CA) and its analogs 2-hydroxycinnamaldehyde and 2-benzoyloxycinnamaldehyde have been reported to possess antitumor activity. CA is also a known Nrf2 activator. In this study, a series of ortho-substituted cinnamaldehyde analogs was synthesized and screened for antiproliferative and thioredoxin reductase (TrxR)-inhibitory activities. Whereas CA was weakly cytotoxic and TrxR inhibiting, hydroxy and benzoyloxy substitutions resulted in analogs with enhanced antiproliferative activity paralleling increased potency in TrxR inactivation. A novel analog, 5-fluoro-2-hydroxycinnamaldehyde, was identified as exhibiting the strongest antitumor effect (GI₅₀ 1.6 μM in HCT 116 cells) and TrxR inhibition (IC₅₀ 7 μM, 1 h incubation with recombinant TrxR). CA and its 2-hydroxy- and 2-benzoyloxy-substituted analogs possessed dual TrxR-inhibitory and Nrf2-inducing effects, both attributed to an active Michael acceptor pharmacophore. At lethal concentrations, TrxR-inhibitory potencies correlated with the compounds' antiproliferative activities. The penultimate C-terminal selenocysteine residue was shown to be a possible target. Conversely, at sublethal concentrations, these agents induced an adaptive antioxidant response through Nrf2-mediated upregulation of phase II enzymes, including TrxR induction. We conclude from the results obtained that TrxR inactivation contributes at least partly to cinnamaldehyde cytotoxicity. These Michael acceptor molecules can potentially be exploited for use in different concentrations in chemotherapeutic and chemopreventive strategies.     

Applications of CRISPR/Cas9 technology for modification of the plant genome

Genetica - The CRISPR/Cas (Clustered regularly interspaced short palindromic repeats/ CRISPR associated protein 9) system was discovered in bacteria and archea as an acquired immune response to...     

5-Aminoimidazole-4-carboxamide-1-β-4-ribofuranoside (AICAR) enhances the efficacy of rapamycin in human cancer cells

mTOR – the mammalian/mechanistic target of rapamycin – has been implicated as a key signaling node for promoting survival of cancer cells. However, clinical trials that have targeted mTOR with rapamycin or rapamycin analogs have had minimal impact. In spite of the high specificity of rapamycin for mTOR, the doses needed to suppress key mTOR substrates have proved toxic. We report here that rapamycin when combined with AICAR – a compound that activates AMP-activated protein kinase makes rapamycin cytotoxic rather than cytostatic at doses that are tolerated clinically. AICAR by itself is able to suppress mTOR complex 1 (mTORC1), but also stimulates a feedback activation of mTORC2, which activates the survival kinase Akt. However, AICAR also suppresses production of phosphatidic acid (PA), which interacts with mTOR in a manner that is competitive with rapamycin. The reduced level of PA sensitizes mTORC2 to rapamycin at tolerable nano-molar doses leading reduced Akt phosphorylation and apoptosis. This study reveals how the use of AICAR enhances the efficacy of rapamycin such that rapamycin at low nano-molar doses can suppress mTORC2 and induce apoptosis in human cancer cells at doses that are clinically tolerable.     

Identification and optimization of small molecule antagonists of vasoactive intestinal peptide receptor-1 (VIPR1)

Identification, synthesis and structure-activity relationship of small-molecule VIPR1 antagonists encompassing two chemical series are described.     

Effect of a synbiotic yogurt on levels of fecal bifidobacteria, clostridia, and enterobacteria

While ingestion of synbiotic yogurts containing Bifidobacterium animalis subsp. lactis and inulin is increasing, their effect on certain microbial groups in the human intestine is unclear. To further investigate this, a large-scale, crossover-design, placebo-controlled study was utilized to evaluate the effect of a synbiotic yogurt containing B. animalis subsp. lactis Bb-12 and inulin on the human intestinal bifidobacteria, clostridia, and enterobacteria. Fecal samples were collected at 14 time points from 46 volunteers who completed the study, and changes in the intestinal bacterial levels were monitored using real-time PCR. Strain Bb-12 could not be detected in feces after 2 weeks of washout. A live/dead PCR procedure indicated that the Bb-12 strain detected in the fecal samples was alive. A significant increase (P < 0.001) in the total bifidobacterial numbers was seen in both groups of subjects during the final washout period compared to the prefeeding period. This increase in total bifidobacteria corresponded with a significant decrease (P < 0.05) in numbers of clostridia but not enterobacteria. No significant differences in numbers of bifidobacteria, clostridia, or enterobacteria were observed between the probiotic and placebo groups during any of the feeding periods. However, subgrouping subjects based on lower initial bifidobacterial numbers or higher initial clostridial numbers did show corresponding significant differences between the synbiotic yogurt and placebo groups. This was not observed for a subgroup with higher initial enterobacterial numbers. While this synbiotic yogurt can increase bifidobacterial numbers and decrease clostridial numbers (but not enterobacterial numbers) in some individuals, it cannot modulate these microbial groups in the majority of individuals.     

Schwann cell-specific JAM-C-deficient mice reveal novel expression and functions for JAM-C in peripheral nerves

Junctional adhesion molecule-C (JAM-C) is an adhesion molecule expressed at junctions between adjacent endothelial and epithelial cells and implicated in multiple inflammatory and vascular responses. In addition, we recently reported on the expression of JAM-C in Schwann cells (SCs) and its importance for the integrity and function of peripheral nerves. To investigate the role of JAM-C in neuronal functions further, mice with a specific deletion of JAM-C in SCs (JAM-C SC KO) were generated. Compared to wild-type (WT) controls, JAM-C SC KO mice showed electrophysiological defects, muscular weakness, and hypersensitivity to mechanical stimuli. In addressing the underlying cause of these defects, nerves from JAM-C SC KO mice were found to have morphological defects in the paranodal region, exhibiting increased nodal length as compared to WTs. The study also reports on previously undetected expressions of JAM-C, namely on perineural cells, and in line with nociception defects of the JAM-C SC KO animals, on finely myelinated sensory nerve fibers. Collectively, the generation and characterization of JAM-C SC KO mice has provided unequivocal evidence for the involvement of SC JAM-C in the fine organization of peripheral nerves and in modulating multiple neuronal responses.     

Amido binding to ReO core: Synthesis, structure and intermolecular interactions

The light green coloured complexes of general formula [Re^VO(L)Cl(OH₂)]Cl have been synthesised in good yields by reacting [Re^VOCl₃(AsPh₃)₂] with HL in dichloromethane in dinitrogen atmosphere. Here, L⁻ is the deprotonated form of N,N-bis(2-pyridylmethyl)amine (HL¹); N-(2-pyridylmethyl)-N′,N′-dimethylethylenediamine (HL²) and N-(2-pyridylmethyl)-N′,N′-diethylethylenediamine (HL³). Single crystal X-ray structure determination of [Re^VO(L¹)Cl(OH₂)]Cl confirms the amido binding of ReO³⁺ species. In the solid state of [Re^VO(L¹)Cl(OH₂)]Cl, the coordinated and counter chloride ions are engaged in Re-Cl…H-C(ring), Cl…H-C(ring) and Re-(OH₂)…Cl hydrogen bonding and forming of a supramolecular network in the solid state. The subunit of the supramolecular network consists of one eight-membered and two nine-membered hydrogen bonded rings. The average diameters of eight-membered and nine-membered rings are ∼3.70 and ∼5.26 Å, respectively.