A Deep Reinforcement Learning Approach to Droplet Routing for Erroneous Digital Microfluidic Biochips.

Digital microfluidic biochips (DMFBs), which are used in various fields like DNA analysis, clinical diagnosis, and PCR testing, have made biochemical experiments more compact, efficient, and user-friendly than the previous methods. However, their reliability is often compromised by their inability to adapt to all kinds of errors. Errors in biochips can be categorized into two types: known errors, and unknown errors. Known errors are detectable before the start of the routing process using sensors or cameras. Unknown errors, in contrast, only become apparent during the routing process and remain undetected by sensors or cameras, which can unexpectedly stop the routing process and diminish the reliability of biochips. This paper introduces a deep reinforcement learning-based routing algorithm, designed to manage not only known errors but also unknown errors. Our experiments demonstrated that our algorithm outperformed the previous ones in terms of the success rate of the routing, in the scenarios including both known errors and unknown errors. Additionally, our algorithm contributed to detecting unknown errors during the routing process, identifying the most efficient routing path with a high probability.

Minimization of MEDA Biochip-Size in Droplet Routing.

With the increasing demand for fast, accurate, and reliable biological sensor systems, miniaturized systems have been aimed at droplet-based sensor systems and have been promising. A micro-electrode dot array (MEDA) biochip, which is one kind of the miniaturized systems for biochemical protocols such as dispensing, dilutions, mixing, and so on, has become widespread due to enabling dynamical control of the droplets in microfluidic manipulations. In MEDA biochips, the electrowetting-on-dielectric (EWOD) technique stands out since it can actuate droplets with nano/picoliter volumes. Microelectrode cells on MEDA actuate multiple droplets simultaneously to route locations for the purpose of the biochemical operations. Taking advantage of the feature, droplets are often routed in parallel to achieve high-throughput outcomes. Regarding parallel manipulation of multiple droplets, however, the droplets are known to be initially placed at a distant position to avoid undesirable mixing. The droplets thus result in traveling a long way for a manipulation, and the required biochip size for routing is also enlarged. This paper proposes a routing method for droplets to reduce the biochip size on a MEDA biochip with the allowance of splitting during routing operations. We mathematically derive the routing problem, and the experiments demonstrate that our proposal can significantly reduce the biochip size by 70.8% on average, compared to the state-of-the-art method.

Precometary organic matter: A hidden reservoir of water inside the snow line.

The origin and evolution of solar system bodies, including water on the Earth, have been discussed based on the assumption that the relevant ingredients were simply silicates and ices. However, large amounts of organic matter have been found in cometary and interplanetary dust, which are recognized as remnants of interstellar/precometary grains. Precometary organic matter may therefore be a potential source of water; however, to date, there have been no experimental investigations into this possibility. Here, we experimentally demonstrate that abundant water and oil are formed via the heating of a precometary-organic-matter analog under conditions appropriate for the parent bodies of meteorites inside the snow line. This implies that H2O ice is not required as the sole source of water on planetary bodies inside the snow line. Further, we can explain the change in the oxidation state of the Earth from an initially reduced state to a final oxidized state. Our study also suggests that petroleum was present in the asteroids and is present in icy satellites and dwarf planets.

An automated laser fluorination technique for high-precision analysis of three oxygen isotopes in silicates.

RATIONALE: The three oxygen isotopes in terrestrial/extraterrestrial silicates can provide geochemical and cosmochemical information about their origin and secondary processes that result from isotopic exchange. A laser fluorination technique has been widely used to extract oxygen from silicates for δ17 O and δ18 O measurements by isotope ratio mass spectrometry. Continued improvement of the techniques is still important for high-precision measurement of oxygen-isotopic ratios. METHODS: We adopted an automated lasing technique to obtain reproducible fluorination of silicates using a CO2 laser-BrF5 fluorination system connected online to an isotope ratio mass spectrometer. The automated lasing technique enables us to perform high-precision analysis of the three oxygen isotopes of typical reference materials (e.g., UWG2 garnet, NBS28 quartz and San Carlos olivine) and in-house references (mid-ocean ridge basalt glass and obsidian). The technique uses a built-in application of laser control with which the laser power can be varied in a programmed manner with a defocused beam which is in a fixed position. RESULTS: The oxygen isotope ratios of some international reference materials analyzed by the manual lasing technique were found to be isotopically lighter with wider variations in δ18 O values, whereas those measured by the automated lasing technique gave better reproducibility (less than 0.2‰, 2SD). The Δ17 O values, an excess of the δ17 O value relative to the fractionation line, also showed high reproducibility (±0.02‰, 2SD). CONCLUSIONS: The system described herein provides high-precision δ17 O and δ18 O measurements of silicate materials. The use of the automated lasing technique followed by careful and controlled purification procedures is preferred to achieve satisfactory isotopic ratio results.

Dual inhibition of Cdc2 protein kinase activation during apoptosis in Xenopus egg extracts.

When intracellular damage accumulates in proliferating somatic cells, the cell cycle usually arrests in G1 or G2 in a checkpoint-dependent manner, either to repair the damage or to die by apoptosis. In contrast, early embryonic cells lack checkpoint-mediated cell-cycle arrest, and it is not clear whether apoptosis in early embryonic cells occurs at a specific cell cycle stage or at random points. Here, we examined the functional molecular link between the embryonic cell cycle and apoptosis using Xenopus egg extracts. When apoptosis was induced in egg extracts by addition of exogenous cytochrome c during cell-cycle progression, cyclin B accumulation was inhibited, Cdc2 was not activated, and the cell cycle arrested at interphase. However, addition of recombinant cyclin B failed to activate Cdc2 due to the strong inhibitory phosphorylation of Cdc2 Tyr15 in apoptotic egg extracts. We found that endogenous Cdc25C, which activates the Cdc2-cyclin B complex by dephosphorylating Cdc2 Tyr15, was inactivated by caspase-mediated cleavage at two sites in the N-terminal regulatory domain. When the hyperactive Cdc25A catalytic fragment was added together with recombinant cyclin B to artificially dephosphorylate Cdc2 Tyr15, M-phase induction was restored in apoptotic egg extracts, indicating that the blockage of cyclin B accumulation and the caspase-mediated inactivation of Cdc25C dually inhibited Cdc2 activation. Apoptosis induction in cytostatic factor-arrested metaphase egg extracts resulted in inactivation of Cdc2 without cyclin B degradation. These results suggest that apoptotic inactivation of Cdc25C plays an important role in arresting the embryonic cell cycle at interphase during apoptosis.

Maturation-associated Dbf4 expression is essential for mouse zygotic DNA replication.

Cdc7 is an S-phase-promoting kinase (SPK) that is required for the activation of replication initiation complex assembly because it phosphorylates the MCM protein complex serving as the replicative helicase in eukaryotic organisms. Cdc7 activity is undetectable in immature mouse GV oocytes, although Cdc7 protein is already expressed at the same level as in mature oocytes or early one-cell embryos at zygotic S-phase, in which Cdc7 kinase activity is clearly detectable. Dbf4 is a regulatory subunit of Cdc7 and is required for Cdc7 kinase activity. Dbf4 is not readily detectable in immature GV oocytes but accumulates to a level similar to that in one-cell embryos during oocyte maturation, suggesting that Cdc7 is already activated in unfertilized eggs (metaphase II). RNAi-mediated knockdown of maternal Dbf4 expression prevents the maturation-associated increase in Dbf4 protein, abolishes the activation of Cdc7, and leads to the failure of DNA replication in one-cell embryos, demonstrating that Dbf4 expression is the key regulator of Cdc7 activity in mouse oocytes. Dormant Dbf4 mRNA in immature GV oocytes is recruited by cytoplasmic polyadenylation during oocyte maturation and is dependent on MPF activity via its cytoplasmic polyadenylation element (CPE) upstream of the hexanucleotide (HEX) in the 3' untranslated region (3'UTR). Our results suggest that Cdc7 is inactivated in immature oocytes, preventing it from the unwanted phosphorylation of MCM proteins, and the oocyte is qualified by proper maturation to proceed following embryogenesis after fertilization through zygotic DNA replication.

Anti-apoptotic activity and proteasome-mediated degradation of Xenopus Mcl-1 protein in egg extracts.

Xenopus egg extracts execute spontaneous apoptosis without the requirement of transcription and translation, and this intrinsic mechanism is supposed to be involved in the physiological elimination of aged eggs. Although apoptosis in this system is carried out by maternally stockpiled materials, the endogenous apoptosis regulators present in egg extracts are still poorly characterized. Here we examined the mRNA expression profiles and apoptosis-regulating functions of 13 Xenopus Bcl-2 family proteins in egg extracts. Among these, we found that endogenous Xenopus Mcl-1 (xMcl-1) physiologically inhibited apoptosis by counteracting the pro-apoptotic activity of endogenous Xenopus Bid in egg extracts. Exogenously added recombinant xMcl-1 was rapidly degraded by proteasome in egg extracts, and we identified the destabilizing region in the N terminus of xMcl-1. Our results suggest that the proteolytic decay of xMcl-1 may change the functional balance between pro- and anti-apoptotic activities of Bcl-2 family proteins, thereby regulating the timing of cytochrome c release in egg extracts.

Nominally hydrous magmatism on the Moon.

For the past 40 years, the Moon has been described as nearly devoid of indigenous water; however, evidence for water both on the lunar surface and within the lunar interior have recently emerged, calling into question this long-standing lunar dogma. In the present study, hydroxyl (as well as fluoride and chloride) was analyzed by secondary ion mass spectrometry in apatite [Ca(5)(PO(4))(3)(F,Cl,OH)] from three different lunar samples in order to obtain quantitative constraints on the abundance of water in the lunar interior. This work confirms that hundreds to thousands of ppm water (of the structural form hydroxyl) is present in apatite from the Moon. Moreover, two of the studied samples likely had water preserved from magmatic processes, which would qualify the water as being indigenous to the Moon. The presence of hydroxyl in apatite from a number of different types of lunar rocks indicates that water may be ubiquitous within the lunar interior, potentially as early as the time of lunar formation. The water contents analyzed for the lunar apatite indicate minimum water contents of their lunar source region to range from 64 ppb to 5 ppm H(2)O. This lower limit range of water contents is at least two orders of magnitude greater than the previously reported value for the bulk Moon, and the actual source region water contents could be significantly higher.

Recruitment of Orc6l, a dormant maternal mRNA in mouse oocytes, is essential for DNA replication in 1-cell embryos.

Mouse oocytes acquire the ability to replicate DNA during meiotic maturation, presumably to ensure that DNA replication does not occur precociously between MI and MII and only after fertilization. Acquisition of DNA replication competence requires protein synthesis, but the identity of the proteins required for DNA replication is poorly described. In Xenopus, the only component missing for DNA replication competence is CDC6, which is synthesized from a dormant maternal mRNA recruited during oocyte maturation, and a similar situation also occurs during mouse oocyte maturation. We report that ORC6L is another component required for acquisition of DNA replication competence that is absent in mouse oocytes. The dormant maternal Orc6l mRNA is recruited during maturation via a CPE present in its 3' UTR. RNAi-mediated ablation of maternal Orc6l mRNA prevents the maturation-associated increase in ORC6L protein and inhibits DNA replication in 1-cell embryos. These results suggest that mammalian oocytes have more complex mechanisms to establish DNA replication competence when compared to their Xenopus counterparts.

Pro-apoptotic activity and mono-/diubiquitylation of Xenopus Bid in egg extracts.

Apoptosis in Xenopus egg extracts is carried out by maternally stockpiled materials, but the contributions of endogenous apoptosis regulators are still poorly characterized. Here we examined the physiological role of Xenopus Bid (xBid), a pro-apoptotic BH3-only member of Bcl-2 family proteins. We found that endogenous xBid was a physiological accelerator of apoptosis in egg extracts. Interestingly, xBid was mono-/diubiquitylated but not degraded by proteasome in egg extracts, and we identified three ubiquitylated Lys residues in the N-terminal propeptide region. Comparison with human Bid suggested that mono-/diubiquitylation is a specific feature of xBid.

Inhibition of apoptosis by ascorbic and dehydroascorbic acids in Xenopus egg extracts.

PURPOSE: The viability of mammalian eggs after ovulation is reported to be improved by the presence of ascorbic acid in the culture medium. However, the pro-survival mechanisms of ascorbic acid are poorly understood. The molecular pathways of apoptosis are evolutionarily conserved among animal species, and Xenopus eggs are technically and ethically more suitable for biochemical analyses than mammalian eggs. We used Xenopus egg cytoplasmic extracts to examine the direct intracellular effects of ascorbic acid. METHODS: Incubation of egg extracts for more than 4 h induces the spontaneous release of cytochrome c from mitochondria. This event triggers the activation of caspases, cleavage of substrate proteins, and execution of apoptosis. Multiple signal transduction pathways including proteolysis and protein phosphorylation are also involved in this process. We examined whether any of these events might be inhibited by the addition of ascorbic acid. RESULTS: Ascorbic acid showed no effect against cytochrome c release, but prevented caspase activation and substrate cleavage. Ascorbic acid also blocked the proteolysis of apoptosis inhibitor proteins and the dephosphorylation of p42 MAP kinase. However, dehydroascorbic acid (oxidized form of ascorbic acid) and acetate (unrelated acid) were equally effective, indicating that these effects were primarily due to their acidity. In addition, dehydroascorbic acid inhibited caspase activities directly in vitro. CONCLUSIONS: The anti-apoptotic effect of ascorbic acid in Xenopus egg extracts is mainly due to cytoplasmic acidification rather than its intracellular antioxidant activity. Instead, oxidative conversion of ascorbic acid into dehydroascorbic acid may inhibit apoptosis through the inhibition of caspases.

p42MAPK-mediated phosphorylation of xEIAP/XLX in Xenopus cytostatic factor-arrested egg extracts.

BACKGROUND: BIR family proteins are evolutionarily conserved anti-apoptotic molecules. One member of Xenopus BIR family proteins, xEIAP/XLX, is a weak apoptosis inhibitor and rapidly degraded in a cell-free apoptotic execution system derived from interphase egg extracts. However, unfertilized eggs are naturally arrested at the metaphase of meiosis II by the concerted activities of Mos-MEK-p42MAPK-p90Rsk kinase cascade (cytostatic factor pathway) and many mitotic kinases. Previous studies suggest that cytostatic factor-arrested egg extracts are more resistant to spontaneous apoptosis than interphase egg extracts in a p42MAPK-dependent manner. We tested whether xEIAP/XLX might be phosphorylated in cytostatic factor-arrested egg extracts, and also examined whether xEIAP/XLX could be functionally regulated by phosphorylation. RESULTS: We found that p42MAPK was the major kinase phosphorylating xEIAP/XLX in cytostatic factor-arrested egg extracts, and three Ser residues (Ser 235/251/254) were identified as p42MAPK-mediated phosphorylation sites. We characterized the behaviors of various xEIAP/XLX mutants that could not be phosphorylated by p42MAPK. However, neither protein stability nor anti-apoptotic ability of xEIAP/XLX was significantly altered by the substitution of Ser with either Ala or Asp at these three sites. CONCLUSION: xEIAP/XLX is physiologically phosphorylated by p42MAPK in Xenopus unfertilized eggs. However, this protein may not serve as an essential mediator of p42MAPK-dependent anti-apoptotic activity.

Hydrous olivine unable to account for conductivity anomaly at the top of the asthenosphere.

The oceanic asthenosphere is observed to have high electrical conductivity, which is highly anisotropic in some locations. In the directions parallel and normal to the plate motion, the conductivity is of the order of 10(-1) and 10(-2) S m(-1), respectively, which cannot be explained by the conductivity of anhydrous olivine. But because hydrogen can be incorporated in olivine at mantle pressures, this observation has been attributed to olivine hydration, which might cause anisotropically high conductivity by proton migration. To examine this hypothesis, here we report the effect of water on electrical conductivity and its anisotropy for hydrogen-doped and undoped olivine at 500-1,500 K and 3 GPa. The hydrous olivine has much higher conductivity and lower activation energy than anhydrous olivine in the investigated temperature range. Nevertheless, extrapolation of the experimental results suggests that conductivity of hydrous olivine at the top of the asthenosphere should be nearly isotropic and only of the order of 10(-2) S m(-1). Our data indicate that the hydration of olivine cannot account for the geophysical observations, which instead may be explained by the presence of partial melt elongated in the direction of plate motion.

Apoptosis-inhibiting activities of BIR family proteins in Xenopus egg extracts.

In many animal species including Xenopus, ovulated eggs possess an intrinsic apoptotic execution system. This program is inhibited for a limited time by some maternal apoptosis inhibitors, although their molecular properties remain uncharacterized. Baculovirus IAP repeat (BIR) family proteins contain evolutionarily conserved BIR domains and play important roles in apoptosis suppression, and are therefore good candidates as maternal apoptosis inhibitors. We identified four maternal BIR family proteins in Xenopus eggs and, using the biochemical advantages of egg extracts, examined their physiological functions. These molecules included two survivin-related proteins, xEIAP/XLX, and a possible ortholog of XIAP named xXIAP. The addition of recombinant xXIAP greatly delayed apoptotic execution, whereas the immunodepletion of endogenous xXIAP significantly accelerated the onset of apoptosis. In contrast, xEIAP/XLX was a poor apoptosis inhibitor, and neither of the survivin orthologs showed anti-apoptotic activity in our assay. Both xEIAP/XLX and xXIAP were degraded by activated caspases, and also by a novel proteolytic system that required the presence of C-terminal RING finger domain but was insensitive to proteasome inhibition. Our data suggest that the regulation of endogenous xXIAP concentration is important for the survival of Xenopus eggs.