Publishing in the Open Access and Open Science era

Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.

Automated Long-Term Monitoring of the Heat-Seeking Behavior of Mosquitoes

Heat is one of the critical cues female mosquitoes use to find vertebrate hosts, particularly in the final step of attraction (touching down on hosts) before the initiation of blood-sucking. To prevent vector-borne diseases such as malaria and dengue fever, which are transmitted via mosquito blood-sucking, it is essential to understand the dynamics and mechanisms of the heat-seeking behavior of mosquitoes. An automated device to quantify CO2-activated heat-seeking behavior with continuous monitoring for up to a week was established. The device is based on the infrared beam break method; it can simultaneously monitor three independent mosquito behaviors (touchdown on a heated target, feeding, and locomotion activity) by using several pairs of infrared laser sensors. This protocol describes brief instructions for the device's construction, directions for use, and possible issues and solutions.

Key Features and Considerations for Using Automated Long-Term Monitoring of Heat-Seeking Behavior of Mosquitoes

Mosquitoes are vectors of various deadly infectious diseases, including malaria and dengue fever. Because these pathogens are transmitted by mosquito blood-feeding behavior, it is important to understand how mosquitoes are attracted to their hosts and how they feed on blood. The simplest method is to observe their behavior with the naked eye or video recording. Furthermore, various devices have been invented to assay mosquito behavior, such as olfactometers. Although each method has distinctive advantages, all have disadvantages, such as limitations in the number of individuals that can be assayed at one time and in observable durations, objective quantification methods, and others. To solve these problems, we have developed an automated device to quantify the carbon dioxide-activated heat-seeking behavior of Anopheles stephensi and Aedes aegypti with continuous monitoring for up to 1 week. This device, which is detailed in an accompanying protocol, can be applied to search for substances and molecules that affect heat-seeking behavior. It may also be applicable to other hematophagous insects.

A simple and affordable method for estimating the fluid volume a mosquito sucks using food dyes

BACKGROUND

Blood-sucking by mosquitoes is an inevitable behavior when pathogens are transmitted among humans. Adenine nucleotides such as ATP are known as phagostimulants for mosquitoes and are widely used to induce and enhance the blood-sucking activity in an artificial manner. Although using ATP solution is convenient to introduce a variety of substances (for example chemicals and pathogens) into the mosquito body via sucking, establishing an easy and cost-effective method to quantify the amount of solution ingested has yet to be reported.

RESULTS

A set of commercial food dyes (green, blue, yellow, and red) was employed in this study. Each dye was added to ATP solution used to colorize the abdomen of Ae. aegypti female mosquitoes after ingestion. The intake of food dyes did not show any toxicity to the mosquitoes, affecting neither ATP-sucking behavior nor survival of the mosquitoes. We observed that quantifying the color intensity of green dye in the mosquito abdomen by spectral analysis, as well as distinguishing the size of the colored abdomen using the naked eye, allowed the estimation of the amount of ingested solution. Using this method, capsaicin, a pungent component of chili peppers, was identified as an aversive tastant that can discourage mosquitoes from sucking the ATP solution.

CONCLUSIONS

Employing commercially available, non-toxic food dyes converted ATP-driven membrane feeding into an easy-to-use method to estimate the amount of solution ingested by mosquitoes. This method can be further applied for a variety of experiments such as introducing a certain quantity of chemical compounds or microbes into the mosquito body.

The Strip-Hippo Pathway Regulates Synaptic Terminal Formation by Modulating Actin Organization at the Drosophila Neuromuscular Synapses

Synapse formation requires the precise coordination of axon elongation, cytoskeletal stability, and diverse modes of cell signaling. The underlying mechanisms of this interplay, however, remain unclear. Here, we demonstrate that Strip, a component of the striatin-interacting phosphatase and kinase (STRIPAK) complex that regulates these processes, is required to ensure the proper development of synaptic boutons at the Drosophila neuromuscular junction. In doing so, Strip negatively regulates the activity of the Hippo (Hpo) pathway, an evolutionarily conserved regulator of organ size whose role in synapse formation is currently unappreciated. Strip functions genetically with Enabled, an actin assembly/elongation factor and the presumptive downstream target of Hpo signaling, to modulate local actin organization at synaptic termini. This regulation occurs independently of the transcriptional co-activator Yorkie, the canonical downstream target of the Hpo pathway. Our study identifies a previously unanticipated role of the Strip-Hippo pathway in synaptic development, linking cell signaling to actin organization.

Development of olfactory projection neuron dendrites that contribute to wiring specificity of the Drosophila olfactory circuit

The antennal lobe (AL) of Drosophila is the first olfactory processing center in which olfactory input and output are spatially organized into distinct channels via glomeruli to form a discrete neural map. In each glomerulus, the axons of a single type of olfactory receptor neurons (ORNs) synapse with the dendrites of a single type of projection neurons (PNs). The AL is an ideal place to study how the wiring specificity between specific types of ORNs and PNs is established during development. During the past two decades, the involvement of diverse molecules in the specification and patterning of ORNs and PNs has been reported. Furthermore, local interneurons-another component of glomeruli-have been recently catalogued and their functions have been gradually dissected. Although there is accumulating knowledge about the involvement of these three cell types in the wiring specificity of the olfactory system, in this review, we focus especially on the development of PN dendrites.

Drosophila Strip serves as a platform for early endosome organization during axon elongation

Early endosomes are essential for regulating cell signalling and controlling the amount of cell surface molecules during neuronal morphogenesis. Early endosomes undergo retrograde transport (clustering) before their homotypic fusion. Small GTPase Rab5 is known to promote early endosomal fusion, but the mechanism linking the transport/clustering with Rab5 activity is unclear. Here we show that Drosophila Strip is a key regulator for neuronal morphogenesis. strip knockdown disturbs the early endosome clustering and Rab5-positive early endosomes become smaller and scattered. Strip genetically and biochemically interacts with both Glued (the regulator of dynein-dependent transport) and Sprint (the guanine nucleotide exchange factor for Rab5), suggesting that Strip is a molecular linker between retrograde transport and Rab5 activation. Overexpression of an active form of Rab5 in strip mutant neurons suppresses the axon elongation defects. Thus, Strip acts as a molecular platform for the early endosome organization that plays important roles in neuronal morphogenesis.

Distinct susceptibility of developing neurons to death following Bax overexpression in the chicken embryo

Bax is a proapoptotic protein that is required for programmed cell death (PCD) of many neuronal populations. Here we show that, during an early period of retinal PCD and in naturally occurring sensory and motor neuron (MN) death in the spinal cord, Bax delivery results in enhanced death of these neural populations. In contrast, Bax overexpression fails to enhance an early phase of MN death that occurs in the cervical spinal cord, although overexpressed Bax appears to be activated in dying MNs. Bax overexpression does not also affect the survival of immature neurons prior to the PCD period. Taken together, these data provide the first in vivo evidence suggesting that Bax appears to act selectively as an executioner only in neurons undergoing PCD. Furthermore, although Bax appears to mediate the execution pathway for PCD, the effect of Bax overexpression on susceptibility to death differs between different neuronal populations.

New bisdesmosidic triterpene saponins from the roots of Pulsatilla chinensis

Further phytochemical analysis aimed at the triterpene saponin constituents of the roots of Pulsatilla chinensis has resulted in the isolation of four new bisdesmosidic triterpene saponins whose aglycons are based on the lupane skeleton (1-4), together with three known saponins (5-7). The structures of the new compounds were determined by spectroscopic analysis and acid-catalyzed hydrolysis.

Flavonol glycosides and steroidal saponins from the leaves of Cestrum nocturnum and their cytotoxicity

Phytochemical analysis of the leaves of Cestrum nocturnum (Solanaceae) resulted in the isolation of two new flavonol glycosides (1, 2) and seven steroidal saponins (3-9), including four new ones (4, 6, 7, and 9). The structures of the new compounds were determined by spectroscopic analysis, including 2D NMR data, and the results of hydrolytic cleavage. Cytotoxic activities of the isolated compounds against human oral squamous cell carcinoma-(HSC-2) cells and normal human gingival fibroblasts are reported.

A new factor from Bacillus mesentericus which promotes the growth of Bifidobacterium

It was reported previously that supernatants of cultures of Bacillus mesentericus TO-A promote the growth of Bifidobacterium species. In this study, a new growth-promoting factor, BM-1, was purified from the supernatant of such a culture and its chemical structure was determined. BM-1 was identified as 3,3-dihydroxyazetidine, and it promoted the growth of several strains of Bifidobacterium.

Direct detection of antipyrine metabolites in rat urine by (13)C labeling and NMR spectroscopy

Antipyrine is a useful probe to evaluate variation of in vivo activities of oxidative hepatic drug-metabolizing enzymes. Here we describe a new approach using (13)C labeling and NMR spectroscopy for the direct and simultaneous detection of all phase I and phase II metabolites of antipyrine in rat urine. [C-methyl-(13)C]Antipyrine was synthesized and administered orally to rats (100 mg/kg), and the 0- to 24-h postdose urine was analyzed by 100-MHz (13)C NMR spectroscopy under the conditions of distortionless enhancement by polarization transfer without any pretreatments such as deconjugation, chromatographic separation, and solvent extraction. Consequently, all the major metabolites in urine were successfully detected with favorable signal-to-noise ratios in the limited acquisition time (30 min). The assignments of the resonances were performed by enzymic modification and spiking authentic samples. The reproducibility of the NMR detection was sufficient for the quantitative evaluation of the metabolic profile. Effects of 3-methylcholanthrene on antipyrine metabolism were examined by this approach to evaluate variation of in vivo phase I and phase II metabolism of antipyrine in rats. The present approach is useful and practical to evaluate variation of in vivo activities of conjugation enzymes as well as oxidation enzymes responsible for the formation of antipyrine metabolites in rats. This direct approach would enhance the value of the antipyrine test because of the simplicity and convenience.

Studies on the stereoselective internal acyl migration of ketoprofen glucuronides using 13C labeling and nuclear magnetic resonance spectroscopy

Internal acyl migration reactions of drug 1beta-O-acyl glucuronides are of interest because of their possible role in covalent binding to serum proteins and consequent allergic reactions as well as their influence on drug disposition. An approach using 13C labeling and nuclear magnetic resonance (NMR) spectroscopy has been used to investigate in situ the kinetics of acyl migration and hydrolysis of 1beta-O-acyl glucuronides of enantiomeric ketoprofens (KPs) in phosphate buffer solutions at 37 degrees C. Apparent first-order degradation of the 1beta-O-acyl glucuronide labeled in the ester carbonyl carbon and the sequential appearance of 2-, 3-, and 4-O-acyl isomers as both alpha- and beta-anomeric forms were observed for each enantiomer. All of the positional isomers and anomers were characterized using two-dimensional NMR spectroscopy (heteronuclear multiple bond correlation, correlated spectroscopy, totally correlated spectroscopy) of the reaction mixtures. The overall degradation rate constants (hr-1) of (R)- and (S)-KP glucuronides were 1.07 +/- 0.154 and 0.55 +/- 0.034, respectively. To evaluate in detail the stereoselective reactivity, a kinetic model describing the rearrangement reactions was constructed, and the kinetics were simulated using a theoretical approach. Only the acyl migration, 1beta-->2beta, was found to have significant stereoselectivity. The rate constants (hr-1) for 1beta-->2beta migration of (R)- and (S)-KP glucuronides were 1.04 +/- 0.158 and 0. 52 +/- 0.029, respectively. The results may suggest that (R)-KP glucuronide could be more susceptible to covalent binding to proteins via acyl migration than the corresponding antipode. This stereoselective reactivity may be responsible for the stereoselective pharmacokinetics of KP. The direct approach using 13C labeling and NMR spectroscopy could also provide insight into the reactivities of other labile drug acyl glucuronides and their isomeric glucuronides.

Proton NMR study on a histone-like protein, HU alpha, from Escherichia coli and its complex with oligo DNAs

It was confirmed that the flexible arm region of HU alpha forms an antiparallel beta-sheet and that all of the residues of phenylalanines, together with some of leucines and/or valines, form a hydrophobic core within the dimer of HU alpha. HU alpha protein alone is thermally labile and melts at 38 degrees C, but it becomes remarkably stabilized and melts at 59 degrees C in the presence of DNA. Several resonances from both HU alpha and DNA perturbed by their complex formation, notably those of His C-2 and C-4 protons, downfield shifted C alpha protons in the antiparallel beta-sheet, as well as Arg C delta and Lys C epsilon protons. The results indicated that a beta-sheet region of HU alpha binds to DNA, and also showed that rapid equilibrium occurs on the NMR time scale between bound and unbound states of HU alpha. A few intermolecular nuclear Overhauser effects (NOEs) were also observed between the protein and H1' protons of DNA in the complex, suggesting that HU alpha binds primarily to the minor groove of DNA.

Conformational recognition of RA-XII by 80S ribosomes: a differential line broadening study in 1H NMR spectroscopy

1H NMR spectroscopy has been used to demonstrate specific binding of rat 80S ribosomes to the major conformer of an antitumor bicyclic hexapeptidic glucoside, RA-XII, isolated from Rubia cordifolia, in a fast exchange process.

[Application of 13C label-nuclear magnetic resonance (NMR) tracer techniques to clinical chemistry. Metabolic rate of benzoic acid to hippuric acid]

A new tracer technique, in which a 13C-labeled compound as a biological tracer and 13C nuclear magnetic resonance (NMR) as an analytical tool are used, is proposed. In order to verify the applicability of the method to clinical chemistry. [1-13C]benzoic acid was administered and [1'-13C]hippuric acid excreted in the urine was quantitated by NMR, by using [1-13C]hippuric acid as an internal standard.