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AbstractIsolation of high-quality RNA from abaca is very challenging due to the presence of polyphenols, polysaccharides, and its high fiber content. In this study, we compared six extraction methods across three tissue types and different developmental stages (in-vitro-grown young versus field-grown mature tissue). The Invitrogen PureLink RNA kit proved to be the most efficient in extracting RNA from young abaca tissues (leaves, pseudostem, and corm). The quality of RNA extracted from young tissues was further assessed by RNA-seq applications, with raw sequencing reads mapping back to the M. textilis reference genome at rates of 86.0%–90.4%. The SDS-TRIzol-method modified with an added on-column DNAse I treatment was used to extract RNA from mature tissues (leaves, midrib, and pseudostem). RNA isolated from five M. textilis cultivars and across three mature tissue types showed RNA yield per 100 mg of fresh weight ranges from 0.57 to 10.94 µg and RNA integrity number (RIN) scores of more than 7.0 for all tissue types. Our improved SDS-Trizol method for RNA extraction described here is simple and yields good quality RNAs from mature abaca tissues while the PureLink RNA kit is suitable for extracting RNA from young abaca samples amenable to RT-qPCR and next-generation sequencing studies. [ABSTRACT FROM AUTHOR]

RNA quality and integrity are critical for many studies in plant molecular biology. However, extracting high-quality RNA from cereal grains is challenging due to the presence of polysaccharides, polyphenols, and other compounds that bind or coprecipitate with RNA particles. To address this, we introduced an initial purification step into the Tri Reagent Solution protocol, which effectively eliminated starch and other contaminants. The performance of this modified protocol was then compared with five other RNA extraction methods, including those based on Tri Reagent Solution and the Direct-zol RNA Miniprep Plus Kit. Introducing our method modification prior to homogenization with Tri Reagent Solution successfully yielded total RNA with both high quality (RIN values ranging from 9.50 to 9.70) and high efficiency, making it suitable for both mRNA extraction using the Dynabeads mRNA Purification Kit and library preparation for transcriptome sequencing by long-read methods, such as Oxford Nanopore Technologies. The protocol was successfully applied to total RNA extraction from rye grains at 14 and 21 days after pollination. This study demonstrates that improving the Tri Reagent Solution protocol through initial purification enables the extraction of high-quality RNA from rye grains. [ABSTRACT FROM AUTHOR]

Modern tomatoes produce colorful mature fruits, but many wild tomato ancestors form green or gray green ripe fruits. Here, tomato cultivar 'Lvbaoshi' (LBS) that produces green ripe fruits was found to contain three recessive loci responsible for fruit development. The colorless peel of LBS fruits was caused by a 603 bp deletion in the promoter of SlMYB12. The candidate genes of the remaining two loci were identified as STAY-GREEN 1 (SlSGR1) and PHYTOENE SYNTHASE 1 (SlPSY1). SGR1 and PSY1 co-suppression by RNAi converted the pink fruits into green ripe fruits in transgenic plants. An amino acid change in PSY1 and a deletion in the promoter of SGR1 were also identified in several wild tomatoes bearing green or gray ripe fruits. Overexpression of PSY1 from green ripe fruit wild tomatoes in LBS plants could only partially rescue the green ripe fruit phenotype of LBS, and transgenic lines expressing ProSGR1 :: SGR1 from Solanum pennellii also failed to convert purple-flesh into red-flesh fruits. This work uncovers a novel regulatory mechanism by which SlMYB12 , SlPSY1 , and SlSGR1 control fruit color in cultivated and some wild tomato species. [ABSTRACT FROM AUTHOR]

This study presents a comparative analysis of AlGalnAs buried heterostructure laser diodes by using dual-channel ridge-waveguides. Different shaped channels, including bowl shaped groove and vertical groove, are explored. Using a vertical groove structure, we achieved an output power of 90 mW at 25 °C with a threshold current of only 4 mA. This represents a 3.6-fold increase in output power compared to the BH-DFB structure. At a high temperature of 85 °C, the laser maintains a side-mode suppression ratio of over 45 dB at the maximum power point. The laser's relative intensity noise in the 0–40 GHz frequency range is less than −162.8 dB/Hz when operated at 300 mA with the chip butterfly packaged. These findings underscore the robustness, reliability, and high-performance capabilities of the developed DFB laser, highlighting its potential for various practical applications. [ABSTRACT FROM AUTHOR]

We describe the design procedure, optimization, and fabrication cycle of an index-pattern FP laser on an InP platform. The design parameters of the ridge and reflector (based on slots) are extracted through simulations. In addition, the performance of reflectors with varying slot widths is analyzed. Subsequently, the extracted parameters are used in a rate equation model to predict the performance of the laser in terms of its L $ - $ I characteristics and the sidemode suppression ratio (SMSR). Moreover, the simulated results are compared with the experimental characterization of lasers fabricated with estimated design parameters revealing that the index-pattern laser with 0.3 $\mu $m slot width delivers the best performance by demonstrating a threshold current of ∼30 mA and $\text{SMSR} > \text{30 dB}$.

RNA isolation is an important step in any transcriptome-based functional genomics study, and the quality and quantity of RNA are crucial for downstream applications like gene expression. Since plant cells contain diverse metabolites, such as polyphenols, starch, etc., isolation of pure-quality RNA is always a challenging task. Specialized plant tissues, such as underground storage organs of potato, turnip, beet, carrot, and other crops, are extremely rich in starch and other secondary metabolites. RNA isolation from these tissues with commonly used reagents (e.g., Trizol) or commercial kits often results in inferior quality and quantity of RNA unsuitable for downstream applications. In the present study, a modified CTAB and SDS-based homogenization procedure amalgamated with the routinely used phase separation procedure has been employed for RNA isolation. High-quality RNA from multiple tissues, especially plant underground storage organs, was obtained with an absorption (A260/A280 and A260/A230) value of 1.80–2.00 and ~ 2.00, respectively. In order to evaluate the suitability of isolated RNA in downstream applications, first-strand cDNA was synthesized and used to amplify seven genes considered as the standard reference genes for different plant storage tissues. RNA isolation from cold-stored potato tuber and gene expression studies also demonstrated suitability and wide applicability of this protocol. Overall, the results indicated better efficacy of the protocol employed in the present study than the existing resource-demanding RNA isolation methods available for potato and other secondary metabolite-rich plant storage organs. [ABSTRACT FROM AUTHOR]

This article explores the genetic factors that influence the coloration of ripe tomatoes, with a focus on the transition from green to red fruit. The study identifies three specific genes that play a role in determining fruit color, and mutations in these genes can result in green ripe fruit. The research also investigates the genetic mechanisms behind green fruit coloration in wild tomato species. Understanding these genetic factors is important for agricultural breeding programs and provides insights into the evolution of fruit color in tomatoes. The study found that the downregulation of certain proteins in pink fruit cultivars can transform the fruit into green ripe fruit. Additionally, genetic variations in other genes contribute to the green or gray-green coloration of ripe fruit in wild tomato species. The study also identifies disruptions in the lycopene biosynthesis pathway and regulatory factors as contributors to green fruit development. These findings have implications for breeding programs and highlight the complexity of fruit ripening regulation. [Extracted from the article]

We have introduced the comprehensive optical-to-noise ratio (OSNR) to investigate simultaneously the effects of all three major linear noise sources in distributed Raman fiber amplifier (DRFA). The total noise power contains double Rayleigh backscattering (DRB) noise, amplified spontaneous emission (ASE) noise, and relative intensity noise (RIN). Also, we have introduced an approximated gain profile approach, which helps in evaluating the OSNR for higher-order pumping (HOP) configuration for backward, forward, and bidirectional DRFA schemes. Finally, by applying the dynamic and static full-numerical computations on a system of eight wavelength division multiplexing (WDM) channels (for amplifier lengths of 70, 140, and 210 km), we demonstrated that for RIN frequencies greater than 100 kHz, the higher-order bidirectional pumping scheme exceeds the backward schemes by 12 dB. [ABSTRACT FROM AUTHOR]

Thrombosis, or the formation of blood clots, can lead to serious medical conditions such as stroke, heart attack, and deep vein thrombosis. The purinoreceptor P2Y12 plays a critical role in the thrombotic pathway and is targeted for therapy to prevent clot formation. However, it is essential to balance the regulation of thrombosis to avoid adverse situations. This study focuses on the P2Y12 receptor and aims to discern the protein residue network and differentiate residues based on their intramolecular interactions. The study utilized a statistical analysis to characterize the significant residues involved in ligand interaction, which helps to identify critical residues that are essential for the function of the receptor. A parametric analysis of interactions of residues in the intraprotein interaction was conducted, which revealed significant residue‐based contacts that facilitate protein interactions. By examining the interactions between residues, the mechanisms underlying protein interactions were studied and the importance of specific residues in facilitating these interactions was determined. This research provides important information on P2Y12, and the findings based on the network based significance of interacting residues may contribute to the development of new therapies that target the receptor to prevent clot formation while maintaining a balance in thrombosis regulation to avoid adverse outcomes. Ultimately, this study could lead to improved treatments for thrombotic disorders and better patient outcomes. [ABSTRACT FROM AUTHOR]

Spontaneous mutations associated with the tomato transcription factors COLORLESS NON-RIPENING (SPL-CNR), NON-RIPENING (NAC-NOR), and RIPENING-INHIBITOR (MADS-RIN) result in fruit that do not undergo the normal hallmarks of ripening but are phenotypically distinguishable. Here, we expanded knowledge of the physiological, molecular, and genetic impacts of the ripening mutations on fruit development beyond ripening. We demonstrated through phenotypic and transcriptome analyses that Cnr fruit exhibit a broad range of developmental defects before the onset of fruit ripening, but fruit still undergo some ripening changes similar to wild type. Thus, Cnr should be considered as a fruit developmental mutant and not just a ripening mutant. Additionally, we showed that some ripening processes occur during senescence in the nor and rin mutant fruit, indicating that while some ripening processes are inhibited in these mutants, others are merely delayed. Through gene expression analysis and direct measurement of hormones, we found that Cnr, nor, and rin have alterations in the metabolism and signaling of plant hormones. Cnr mutants produce more than basal levels of ethylene, while nor and rin accumulate high concentrations of abscisic acid. To determine genetic interactions between the mutations, we created for the first time homozygous double mutants. Phenotypic analyses of the double ripening mutants revealed that Cnr has a strong influence on fruit traits and that combining nor and rin leads to an intermediate ripening mutant phenotype. However, we found that the genetic interactions between the mutations are more complex than anticipated, as the Cnr/nor double mutant fruit has a Cnr phenotype but displayed inhibition of ripening-related gene expression just like nor fruit. Our reevaluation of the Cnr, nor, and rin mutants provides new insights into the utilization of the mutants for studying fruit development and their implications in breeding for tomato fruit quality.

We demonstrate a radio-over-fiber-based hybrid wavelength-division-multiplexed/time division multiplexed passive optical network (PON) to transmit 5 Gbps data rate to serve 32 subscribers. A broadband light source (BLS) is realized by mutual injection locking between two Fabry-Perot laser diodes at the transmission section to seed wavelength-division-multiplexed channels. Mutual injection locking technique is used to enhance the performance over single Fabry-Perot laser diode and 15 dB/Hz improvements in relative intensity noise(RIN) is realized in our proposed network system. All-optical up-conversion of a 10-GHz 1.25 Gbps on off keying radio frequency (RF) signal is achieved using one single-arm Mach-Zehnder modulator (MZM). Transmission performance over 25-km single mode fiber is investigated. Low bit error rate with enhanced eye-diagram is obtained in our proposed system. As a result, the radio over fiber (ROF)-based wavelength-division-multiplexed/time division multiplexed PON set up employing mutually injection locked Fabry-Perot laser diodes can be a better choice in high speed long-haul optical communication system. [ABSTRACT FROM AUTHOR]

High-quality mRNA extraction is essential for gene expression assays. In this study, we developed a rapid method (20 min) named FACTS for the extraction of intact RNA from Pseudomonas aeruginosa and compared its performance to established rapid techniques like RNAsnap and CiAR. The RNA integrity, yield, purity and presence of residual genomic DNA were adopted as assessment criteria. Multiple assays for RNA integrity were applied, including the Agilent 2200 TapeStation, QIAxcel capillary electrophoresis, and the newly available Qubit RNA Integrity and Quality (IQ) Assay Kit. The RNA purity and DNA/RNA yield were assessed by spectrophotometry and fluorimetry, respectively. Following Dnase treatment, two-step RT-qPCR for the expression of the rpoD reference gene was performed to evaluate the performance of each method. In terms of RNA integrity, FACTS showed the highest RNA integrity, while in terms of purity, CiAR scored best. RNAsnap resulted in a substantial amount of residual DNA. Pilot experiments for RNA extraction with FACTS from other Gram-negative and Gram-positive bacteria revealed promising results. FACTS is a novel RNA extraction method for rapid highly effective extraction of high-quality RNA from P. aeruginosa and can be used as a cost-efficient alternative to other methods in gene expression studies. [ABSTRACT FROM AUTHOR]

Transcription factors (TFs) are crucial for regulating fruit ripening in tomato (Solanum lycopersicum). The GRAS (GAI, RGA, and SCR) TFs are involved in various physiological processes, but their role in fruit ripening has seldom been reported. We have previously identified a gene encoding GRAS protein named SlFSR (F ruit S helf-life R egulator), which is implicated in fruit ripening by regulating cell wall metabolism; however, the underlying mechanism remains unclear. Here, we demonstrate that SlFSR proteins are localized to the nucleus, where they could bind to specific DNA sequences. SlFSR acts downstream of the master ripening regulator RIN and could collaborate with RIN to control the ripening process by regulating expression of ethylene biosynthesis genes. In SlFSR -CR (CRISPR/Cas9) mutants, the initiation of fruit ripening was not affected but the reduced ethylene production and a delayed coloring process occurred. RNA-sequencing (RNA-seq) and promoter analysis reveal that SlFSR directly binds to the promoters of two key ethylene biosynthesis genes (SlACO1 and SlACO3) and activates their expression. However, SlFSR -CR fruits displayed a significant down-regulation of key rate-limiting genes (SlDXS1 and SlGGPPS2) in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, which may account for the impaired lycopene synthesis. Altogether, we propose that SlFSR positively regulates ethylene biosynthesis and lycopene accumulation, providing valuable insights into the molecular mechanisms underlying fruit ripening. • SlFSR regulates ET biosynthesis by activating the transcription of SlACO1 and SlACO3. • SlFSR regulates carotenoids accumulation by influencing the MEP pathway. • SlFSR and RIN cooperate to regulate the ripening processes in tomato. [ABSTRACT FROM AUTHOR]

High-quality mRNA extraction is essential for gene expression assays. In this study, we developed a rapid method (20 min) named FACTS for the extraction of intact RNA from Pseudomonas aeruginosa and compared its performance to established rapid techniques like RNAsnap and CiAR. The RNA integrity, yield, purity and presence of residual genomic DNA were adopted as assessment criteria. Multiple assays for RNA integrity were applied, including the Agilent 2200 TapeStation, QIAxcel capillary electrophoresis, and the newly available Qubit RNA Integrity and Quality (IQ) Assay Kit. The RNA purity and DNA/RNA yield were assessed by spectrophotometry and fluorimetry, respectively. Following Dnase treatment, two-step RT-qPCR for the expression of the rpoD reference gene was performed to evaluate the performance of each method. In terms of RNA integrity, FACTS showed the highest RNA integrity, while in terms of purity, CiAR scored best. RNAsnap resulted in a substantial amount of residual DNA. Pilot experiments for RNA extraction with FACTS from other Gram-negative and Gram-positive bacteria revealed promising results. FACTS is a novel RNA extraction method for rapid highly effective extraction of high-quality RNA from P. aeruginosa and can be used as a cost-efficient alternative to other methods in gene expression studies.

To induce a Raman-active transition in a material, stimulated Raman scattering (SRS) spectroscopy/microscopy implementations typically rely on two pulsed laser sources. One of their limitations is that not all of the regions of Raman spectra can be investigated, so only some applications can be exploited. In this paper, the noise characterizations of a stimulated Raman scattering spectroscopy/microscopy implementation, based on the insertion of a third pulsed laser source, are provided. The merit of this system is that it is able to explore the large variety of SRS applications. In order to characterize our system, an investigation of different kinds of noises due to the laser sources and electronics sources was carried out. Firstly, the relative intensity noises of three femtosecond laser sources were measured. Secondly, noise characterizations of the detection system were carried out and our findings prove that our SRS microscope is shot noise-limited, demonstrating that the third laser source introduction is well suited and satisfies our purpose. Finally, the statistical properties of the overall image noises are analyzed and discussed. [ABSTRACT FROM AUTHOR]

The problem of isolating high-quality total RNA from intervertebral discs has no recognized solution yet. This is due to the extremely low content of live cells in the samples and the voluminous intercellular matrix. A variety of published protocols focused on isolating RNA from articular cartilage have recommended the use of expensive equipment, enzymatic matrix cleavage, or cell culture. In our study, we used a combination of the traditional QIAzol protocol (Qiagen, Germany) and RNEasy column purification (Qiagen, Germany) to obtain high-quality RNA from post-surgical intervertebral disc fragments. Only a mortar and a pestle were used for grinding, making our method particularly accessible. The isolated RNA with a RIN of ~7 is suitable for studying the expression profile of chondrocytes in situ. RNA-seq analysis of three samples demonstrated cell type ratios to be mostly relevant to intervertebral disc tissues, with over 70% of the chondrocytes of the three subtypes having an admixture of blood-related cells. [ABSTRACT FROM AUTHOR]

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus. In infected cells, its positive-sense RNA genome is translated into polyproteins that are subsequently processed into four nonstructural proteins (nsP1 to 4), the virus-encoded subunits of the RNA replicase. However, for RNA replication, interactions between nsPs and host proteins are also needed. These interactions are mostly mediated through the intrinsically disordered C-terminal hypervariable domain (HVD) in nsP3. Duplicate FGDF motifs in the HVD are required for interaction with mammalian RasGAP SH3-binding proteins (G3BPs) and their mosquito homolog Rin; these interactions are crucial for CHIKV RNA replication. In this study, we inactivated G3BP/Rin-binding motifs in the HVD and inserted peptides containing either native or inactivated G3BP/Rin-binding motifs into flexible regions of nsP1, nsP2, or nsP4. Insertion of native motifs into nsP1 or nsP2 but not into the C terminus of nsP4 activated CHIKV RNA replication in human cells in a G3BP-dependent manner. In mosquito cells, activation also resulted from the insertion of inactive motifs after residue 8 or 466 in nsP2; however, the effect was significantly larger when the inserted sequence contained native motifs. Nonetheless, CHIKV mutants harboring mutations in the HVD and containing insertions of native motifs in nsP2 were not viable in mosquito cells. In contrast, mutant genomes containing native motifs after residue 466 or 618 in nsP2 replicated in BHK-21 cells, with the latter mutant forming infectious progeny. Thus, the binding of G3BPs to nsP2 can support CHIKV RNA replication and restore the infectivity of viruses lacking G3BP-binding motifs in the HVD of nsP3. [ABSTRACT FROM AUTHOR]

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In the Indian philosophical system Vedanta, the composite human being is described in terms of five concentric sheaths surrounding an inner core - the Pancha Kosha (Five Sheaths) model. This model has implications for the discipline of Transactional Analysis insofar as it sheds light on the working of the Adult Ego State and also suggests the process by which autonomy can be achieved. Other concepts of Vedanta relevant to TA are discussed and elaborated, and a Vedantic Ego States Model presented incorporating them into the Classical TA model. The natural longing for intimacy and the growth force of physis are represented in terms of insights from Vedanta. The practice implications of the model are discussed, and also how it can help for personal growth and eventually spiritual progress.

To induce a Raman-active transition in a material, stimulated Raman scattering (SRS) spectroscopy/microscopy implementations typically rely on two pulsed laser sources. One of their limitations is that not all of the regions of Raman spectra can be investigated, so only some applications can be exploited. In this paper, the noise characterizations of a stimulated Raman scattering spectroscopy/microscopy implementation, based on the insertion of a third pulsed laser source, are provided. The merit of this system is that it is able to explore the large variety of SRS applications. In order to characterize our system, an investigation of different kinds of noises due to the laser sources and electronics sources was carried out. Firstly, the relative intensity noises of three femtosecond laser sources were measured. Secondly, noise characterizations of the detection system were carried out and our findings prove that our SRS microscope is shot noise-limited, demonstrating that the third laser source introduction is well suited and satisfies our purpose. Finally, the statistical properties of the overall image noises are analyzed and discussed.

The problem of isolating high-quality total RNA from intervertebral discs has no recognized solution yet. This is due to the extremely low content of live cells in the samples and the voluminous intercellular matrix. A variety of published protocols focused on isolating RNA from articular cartilage have recommended the use of expensive equipment, enzymatic matrix cleavage, or cell culture. In our study, we used a combination of the traditional QIAzol protocol (Qiagen, Germany) and RNEasy column purification (Qiagen, Germany) to obtain high-quality RNA from post-surgical intervertebral disc fragments. Only a mortar and a pestle were used for grinding, making our method particularly accessible. The isolated RNA with a RIN of ~7 is suitable for studying the expression profile of chondrocytes in situ. RNA-seq analysis of three samples demonstrated cell type ratios to be mostly relevant to intervertebral disc tissues, with over 70% of the chondrocytes of the three subtypes having an admixture of blood-related cells.

MADS-domain transcription factor RIPENING INHIBITOR (RIN) is the global regulator of tomato Solanum lycopersicum L. fruit ripening. RIN controls the cascade of fleshy fruit ripening reactions on several levels: it activates the expression of genes encoding other regulation proteins and genes of ethylene biosynthesis (initiation of ethylene-dependent signaling pathways); it directly activates transcription of genes of carotenoid biosynthesis, aroma compounds, carbohydrate metabolism and cell wall-modifying enzymes (by ethylene independent regulation); RIN also involved in epigenetic control of fleshy fruit ripening. Originally discovered in tomato, RIN homologs have now been described for many fleshy fruit crops. The review considers the molecular features of the RIN and homologues MADS-domain transcription factors in different plant species that have similar function of fleshy fruit ripening control and sharing the same evolutionary history. The structure, spatial-temporal expression, and target genes of these regulators are characterized. Using the example of monocotyledonous and dicotyledonous plants that form fleshy fruits, such as tomato, banana, pepper, grape, and strawberry, it has been shown that MADS proteins of the SEPALLATA subfamily play a central role in the complex transcriptional regulation of the ripening cascade of both climacteric and non-climacteric fruits. [ABSTRACT FROM AUTHOR]

BackgroundThe 3-gene signature of periostin, chloride channel accessory 1 (CLCA1), and Serpin β2 (SERPINB2) in airway epithelial brushings is used to classify asthma into TH2-high and TH2-low endotypes. Little is known about the utility of gene profiling in sputum as a molecular phenotyping method.ObjectiveWe sought to determine whether gene profiling in sputum cells can identify T(H)2-high and T(H)2-low subtypes of asthma.MethodsIn induced sputum cell pellets from 37 asthmatic patients and 15 healthy control subjects, PCR was used to profile gene expression of the epithelial cell signature of IL-13 activation (periostin, CLCA1, and SERPINB2), TH2 genes (IL4, IL5, and IL13), and other genes associated with airway TH2 inflammation.ResultsGene expression levels of CLCA1 and periostin, but not SerpinB2, were significantly higher than normal in sputum cells from asthmatic subjects. Expression levels of IL-4, IL-5, and IL-13 were also significantly increased in asthmatic patients and highly correlated within individual subjects. By combining the expression levels of IL-4, IL-5, and IL-13 in a single quantitative metric ("T(H)2 gene mean"), 26 (70%) of the 37 asthmatic patients had T(H)2-high asthma, which was characterized by more severe measures of asthma and increased blood and sputum eosinophilia. TH2 gene mean values tended to be stable when initial values were very high or very low but fluctuated above or below the T(H)2-high cutoff when initial values were intermediate.ConclusionIL-4, IL-5, and IL-13 transcripts are easily detected in sputum cells from asthmatic patients, and their expression levels can be used to classify asthma into T(H)2-high and T(H)2-low endotypes.

Since the polarization non-reciprocity errors are canceled out through optical compensation in dual-polarization interferometric fiber-optic gyroscopes (IFOGs), two ports, namely, the reciprocal and nonreciprocal ports, are both feasible sensing output. In this work, we propose and demonstrate a weighted subtraction method for noise suppression that utilizes the partial correlated two-port signals simultaneously. The relative intensity noise has reduced to 56.2% of its original value in the experiment and agrees with the theoretical anal/ ysis; as a result, the angle random walk is suppressed from 5.7 x 10-2 to 3.2 x 10-2°/√h with a 2-km-long fiber. The improvement on shortand long-term stability performance has been experimentally verified, which makes dual-polarization IFOG configuration promising for many applications.

A level optimization method for the 4-level pulse-amplitude modulation format is proposed. This optimization method is applicable to signal-dependent noise conditions such as the relative intensity noise and amplified spontaneous noise. The proposed optimization was verified by simulation results and an experimental demonstration at 53 Gbaud, showing an improvement of 4 dB.

Spontaneous mutations associated with the tomato transcription factors COLORLESS NON-RIPENING (SPL-CNR), NON-RIPENING (NAC-NOR), and RIPENING-INHIBITOR (MADS-RIN) result in fruit that do not undergo the normal hallmarks of ripening but are phenotypically distinguishable. Here, we expanded knowledge of the physiological, molecular, and genetic impacts of the ripening mutations on fruit development beyond ripening. We demonstrated through phenotypic and transcriptome analyses that Cnr fruit exhibit a broad range of developmental defects before the onset of fruit ripening, but fruit still undergo some ripening changes similar to wild type. Thus, Cnr should be considered as a fruit developmental mutant and not just a ripening mutant. Additionally, we showed that some ripening processes occur during senescence in the nor and rin mutant fruit, indicating that while some ripening processes are inhibited in these mutants, others are merely delayed. Through gene expression analysis and direct measurement of hormones, we found that Cnr, nor, and rin have alterations in the metabolism and signaling of plant hormones. Cnr mutants produce more than basal levels of ethylene, while nor and rin accumulate high concentrations of abscisic acid. To determine genetic interactions between the mutations, we created for the first time homozygous double mutants. Phenotypic analyses of the double ripening mutants revealed that Cnr has a strong influence on fruit traits and that combining nor and rin leads to an intermediate ripening mutant phenotype. However, we found that the genetic interactions between the mutations are more complex than anticipated, as the Cnr/nor double mutant fruit has a Cnr phenotype but displayed inhibition of ripening-related gene expression just like nor fruit. Our reevaluation of the Cnr, nor, and rin mutants provides new insights into the utilization of the mutants for studying fruit development and their implications in breeding for tomato fruit quality.

We report on a detailed analysis of the effect of CW injection in an actively mode-locked laser at 780 nm, on the noise performances of the laser. The optical properties of the emitted pulse train, and the phase and amplitude noise of the RF pulse train generated after photodetection have been characterized with respect to the laser pumping rate, and to the injected power. We show that when injected, the laser exhibits a dramatic improvement of both RF phase noise and power spectrum, but at the expense of a degraded optical relative intensity noise. [ABSTRACT FROM AUTHOR]

Spontaneous mutations associated with the tomato transcription factors COLORLESS NON-RIPENING (SPL-CNR), NON-RIPENING (NAC-NOR), and RIPENING-INHIBITOR (MADS-RIN) result in fruit that do not undergo the normal hallmarks of ripening but are phenotypically distinguishable. Here, we expanded knowledge of the physiological, molecular, and genetic impacts of the ripening mutations on fruit development beyond ripening. We demonstrated through phenotypic and transcriptome analyses that Cnr fruit exhibit a broad range of developmental defects before the onset of fruit ripening, but fruit still undergo some ripening changes similar to wild type. Thus, Cnr should be considered as a fruit developmental mutant and not just a ripening mutant. Additionally, we showed that some ripening processes occur during senescence in the nor and rin mutant fruit, indicating that while some ripening processes are inhibited in these mutants, others are merely delayed. Through gene expression analysis and direct measurement of hormones, we found that Cnr , nor , and rin have alterations in the metabolism and signaling of plant hormones. Cnr mutants produce more than basal levels of ethylene, while nor and rin accumulate high concentrations of abscisic acid. To determine genetic interactions between the mutations, we created for the first time homozygous double mutants. Phenotypic analyses of the double ripening mutants revealed that Cnr has a strong influence on fruit traits and that combining nor and rin leads to an intermediate ripening mutant phenotype. However, we found that the genetic interactions between the mutations are more complex than anticipated, as the Cnr/nor double mutant fruit has a Cnr phenotype but displayed inhibition of ripening-related gene expression just like nor fruit. Our reevaluation of the Cnr , nor , and rin mutants provides new insights into the utilization of the mutants for studying fruit development and their implications in breeding for tomato fruit quality. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) patients could benefit from a more effective treatment than the current FDA-approved options. Because amyloid-beta (Aβ) is thought to play a central role in AD pathogenesis, many experimental drugs attempt to reduce Aβ-induced pathology. Preventing amyloid accumulation may be a more effective strategy than clearing Aβ plaques after they form. If preventing Aβ accumulation can treat or prevent AD, then understanding Aβ primary nucleation may aid rational drug design. This study examines Aβ residue interaction networks and reports network and structural observations that may provide insight into primary nucleation. While many studies identify structural features of Aβ that promote aggregation, this study reports features that may resist primary nucleation by examining Aβ42 studies in more and less polar solvents. In Aβ42 in a less polar solvent (PDB ID: 1IYT), Val24 and Ile31 have higher betweenness and residue centrality values. This may be due to a predicted interaction between Val24 and Ile31. Residues in the central hydrophobic cluster (CHC) of Aβ40 and Aβ42 had significantly higher betweenness values compared to the average betweenness of the structures, highlighting the CHC's reported role in oligomerization. The predicted interaction between Val24 and Ile31 may reduce the likelihood of primary nucleation of Aβ. [ABSTRACT FROM AUTHOR]

High-quality RNA is required for accurate gene expression and transcriptome analysis. The current methods of RNA extraction from berry fruits are either time-consuming or expensive. To simplify the conventional phenol-chloroform based RNA extraction method, we modified the protocol with less steps as well as the removal of the use of phenol. In this protocol, the extraction buffer is composed of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and Dithiothreitol (DTT). The method facilitates efficient removal of polysaccharides and phenolic compounds from both fruit pulp and fruit peel. Additionally, the protocol is phenol-free and less toxic than traditional phenol-containing method. High-quality RNA, with RNA Integrity Number value > 8, isolated by this method is applicable for RNA sequencing and qPCR. Only 3–4 working hours are required for one batch of RNA isolation. • Our method replaces the use of phenol-chloroform with chloroform, making the extraction less toxic. • The bilberry friut RNA is of high-quality and purity with less time input.

Comparative modelling helps compare the structure and functions of a given protein, to track the path of its origin and evolution and also guide in structure-based drug discovery. Presently, this has been applied for modelling the tertiary structure of highly conserved eukaryotic TCTP (translationally controlled tumour protein) which is involved in a plethora of functions during growth and development and also acts as a biomarker for many cancers like lung, breast, and prostate cancer. The modelled TCTP structures of different organisms belonging to the eukaryotic group showed similar spatial arrangement of structural units except loops and similar patterns of root mean square deviation (RMSD), root mean square fluctuation, and radius of gyration (Rg) inspected through molecular dynamics simulations. Essential dynamics (ED) analyses revealed different domains that exhibited different motions for the assistance in its multifunctional properties. Construction of a free-energy landscape (FEL) based on Rg versus RMSD was employed to characterize the folding behaviours of structures and observe that all proteins had nearly similar conformation and topologies, indicating common thermodynamic/kinetic pathways. A physico-chemical interaction study demonstrated the helices and sheets were well stabilized with ample amounts of bonding compared to turns or loops and charged residues were more accessible to solvent molecules. Hence, the current study reveals the important structural features of TCTP that aid in diverse functions in a wide range of organisms, thus extending our knowledge of TCTP and also providing a venue for designing the potent inhibitors against it. [ABSTRACT FROM AUTHOR]

The striatum can be divided into the DLS (dorsolateral striatum) and the VMS (ventromedial striatum), which includes NAcC (nucleus accumbens core) and NAcS (nucleus accumbens shell). Here, we examined differences in electrophysiological properties of MSSNs (medium-sized spiny neurons) based on their location, expression of DA (dopamine) D1/D2 receptors and responses to the μ-opioid receptor agonist, DAMGO {[D-Ala(2)-MePhe(4)-Gly(ol)(5)]enkephalin}. The main differences in morphological and biophysical membrane properties occurred among striatal sub-regions. MSSNs in the DLS were larger, had higher membrane capacitances and lower Rin (input resistances) compared with cells in the VMS. RMPs (resting membrane potentials) were similar among regions except for D2 cells in the NAcC, which displayed a significantly more depolarized RMP. In contrast, differences in frequency of spontaneous excitatory synaptic inputs were more prominent between cell types, with D2 cells receiving significantly more excitatory inputs than D1 cells, particularly in the VMS. Inhibitory inputs were not different between D1 and D2 cells. However, MSSNs in the VMS received more inhibitory inputs than those in the DLS. Acute application of DAMGO reduced the frequency of spontaneous excitatory and inhibitory postsynaptic currents, but the effect was greater in the VMS, in particular in the NAcS, where excitatory currents from D2 cells and inhibitory currents from D1 cells were inhibited by the largest amount. DAMGO also increased cellular excitability in the VMS, as shown by reduced threshold for evoking APs (action potentials). Together the present findings help elucidate the regional and cell-type-specific substrate of opioid actions in the striatum and point to the VMS as a critical mediator of DAMGO effects.

Extraction of high-quality RNA from pancreatic tumors for sequencing purposes is technically challenging, as the pancreas is an organ rich in ribonucleases. The majority of the established RNA isolation protocols for use with primary pancreatic tissue involve perfusion of RNA stabilizing reagent into the pancreatic tissue to protect RNA integrity before extraction. However, the additional time needed for this procedure can actually lead to further RNA degradation. We optimized a protocol suitable for high quality RNA isolation from mouse pancreatic tumors that is a simple, fast, and inexpensive modification of existing methods, combining the use of liquid nitrogen and guanidinium thiocyanate-chloroform extraction. Through this procedure, the mean RNA Integrity Number value obtained for RNA isolated from pancreatic tumors was 9.0, and was reproducibly suitable for RNAseq and qPCR. • a protocol suitable for high quality RNA isolation from mouse pancreatic tumors as well as normal pancreas • combining the use of liquid nitrogen and guanidinium thiocyanate-chloroform extraction

Ethylene signaling pathways regulate several physiological alterations that occur during tomato fruit ripening, such as changes in colour and flavour. The mechanisms underlying the transcriptional regulation of genes in these pathways remain unclear, although the role of the MADS-box transcription factor RIN has been widely reported. Here, we describe a bHLH transcription factor, SlbHLH95, whose transcripts accumulated abundantly in breaker+4 and breaker+7 fruits compared with rin (ripening inhibitor) and Nr (never ripe) mutants. Moreover, the promoter activity of SlbHLH95 was regulated by RIN in vivo. Suppression of SlbHLH95 resulted in reduced sensitivity to ethylene, decreased accumulation of total carotenoids, and lowered glutathione content, and inhibited the expression of fruit ripening- and glutathione metabolism-related genes. Conversely, up-regulation of SlbHLH95 in wild-type tomato resulted in higher sensitivity to ethylene, increased accumulation of total carotenoids, slightly premature ripening, and elevated accumulation of glutathione, soluble sugar, and starch. Notably, overexpression of SlbHLH95 in rin led to the up-regulated expression of fruit ripening-related genes (FUL1 , FUL2 , SAUR69 , ERF4 , and CNR) and multiple glutathione metabolism-related genes (GSH1 , GSH2 , GSTF1 , and GSTF5). These results clarified that SlbHLH95 participates in the regulation of fruit ripening and affects ethylene sensitivity and multiple metabolisms targeted by RIN in tomato. [ABSTRACT FROM AUTHOR]

We investigate the intensity and phase noise properties of GaAs-based 1060 nm oxide-confined single-mode vertical-cavity surface-emitting lasers (VCSELs) and their dependence on slope efficiency and current spreading, parameters that control the achievable output power. We find strong dependence of the linewidth on slope efficiency because it affects the optical resonator loss and therefore the spontaneous emission rate and the photon density. Likewise, we find strong dependence of the relative intensity noise on the slope efficiency since the optical resonator loss controls the photon lifetime, and therefore the damping of the relaxation oscillations. There is no noticeable dependence on transverse current confinement and current spreading. We measure linewidths as small as 6 MHz which we attribute to a small linewidth enhancement factor. This assumption is supported by calculations of the linewidth enhancement factor from optical resonator and optical gain simulations. The dependencies of noise on design parameters are general and therefore valid for single-mode VCSELs at other wavelengths and in other material systems. [ABSTRACT FROM AUTHOR]

Summary: Fruit ripening is governed by a complex regulatory network. Reversible histone methylation and demethylation regulate chromatin structure and gene expression. However, little is known about the involvement of histone demethylases in regulating fruit ripening.Here, we found that the tomato (Solanum lycopersicum) SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerates tomato fruit ripening, which is associated with the upregulated expression of a large number of ripening‐related genes.Integrated analysis of RNA‐seq and chromatin immunoprecipitation followed by sequencing identified 32 genes directly targeted by SlJMJ6 and transcriptionally upregulated with decreased H3K27m3 in SlJMJ6‐overexpressed fruit. Numerous SlJMJ6‐regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation and hormone signaling. Eleven ripening‐related genes including RIPENING INHIBITOR (RIN), 1‐aminocyclopropane 1‐carboxylate synthase‐4 (ACS4), 1‐aminocyclopropane‐1‐carboxylate oxidase 1 (ACO1), pectate lyase (PL) and beta‐galactosidase 4 (TBG4), and a DNA demethylase DML2, were confirmed to be regulated directly by SlJMJ6 through removing H3K27me3.Our results demonstrate that SlJMJ6 is a ripening‐prompting H3K27me3 demethylase that activates the expression of the ripening‐related genes by modulating H3K27me3, thereby facilitating tomato fruit ripening. Our work also reveals a novel link between histone demethylation and DNA demethylation in regulating fruit ripening. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening. [ABSTRACT FROM AUTHOR]

The D4 RIN is the tradable compliance certificate for the biomass‐based diesel (BBD) mandate in the renewable fuel standard (RFS). Understanding the price dynamics of the D4 RIN is important for understanding the RFS because its price sets a ceiling on the ethanol RIN (D6) and because some observers have suggested that RIN price fluctuations are too large to be explained by economic theory. We use option pricing theory to develop a model of the D4 RIN in terms of its economic fundamentals: the spread between the price of biodiesel and petroleum diesel and the status of the biodiesel blenders' tax credit. The resulting D4 fundamental price closely tracks actual D4 prices. We conclude that RIN price volatility arises because of the design of the RFS and intrinsic features of the U.S. fuel supply system. [ABSTRACT FROM AUTHOR]

Background: The increasing cases of non-small cell lung cancer pose a relentless threat to human health. Therefore, using fragment-based drug discovery as the modus operandi, the present study aimed to design small molecule inhibitors for Anaplastic Lymphoma Kinase (ALK) positive Non-Small Cell Lung Cancer (NSCLC) and for its secondary mutation (F1174L). Materials and methods: A total of 12 ALK inhibitors (both FDA and clinical) reported in the literature was utilised in the present study to design the novel and potent ALK inhibitors. Fragment script and BREED of Schrödinger suite was used to generate novel structural combinations. GLIDE algorithm was employed to identify the fragments with high binding affinity to the native and mutant forms of ALK. Screened out fragments were subjected to ADMET analysis. Additionally, the impact of F1174L mutation in the stability of ALK protein was assessed using SDM and I-Mutant tools. RING algorithm was employed to compare the pattern of intramolecular interaction between the native and F1174L ALK protein. Results: A novel hybrid molecule LF16 was identified with better binding, superior CNS activity, higher drug score and low toxicity. Annihilation of intramolecular interactions with Ile 1179, Ile 1170 and Phe1098 were found to be the cause of the destabilizing effect of the mutant protein. Of note, these residues were found to play important roles in the formation of F-core as well as in stabilizing αC-helix, which is important for maintaining the inactive form of ALK. Moreover, Conclusion: We believe that these results could foster the designing and development of novel ALK inhibitors towards the management of crizotinib resistance in the near future. [ABSTRACT FROM AUTHOR]

Quality control (QC) is primordial for determining the efficiency in any downstream genomic applications. There are several steps in the verification of the quality of RNA samples destined for genomic studies. The aim of this research was to determine whether RNA should be discarded at the level of the field lab if it fails preliminary quality control using Optical Density (OD) measurements. In this study, all samples were submitted to rigorous quality control in every stage of work. RNA samples showing poor OD values still gave excellent results in downstream QC and genomic applications. At the end of the quality control exercise, it was observed that the original samples were the same and had not undergone any deterioration along the different stages of handling and manipulation. This paper shows the different and most important stages of quality control on RNA samples (RIN) for an effective down stream application in genomic studies. RNA samples should not be discarded based on preliminary QC from our field labs., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Biomarkers are biological characteristic to measure and evaluate normal and pathological states. To define expression-based molecular biomarkers, high-quality tissue samples are a prerequisite for the preparation of standard RNA. It is already known that RIN number defines the RNA quality, however its relation with A260/280 ratio and Ct value is not defined clearly; therefore, understanding an association will provide a reliable method for describing RNA quality. Multiple cryopreserved human tumor tissue types from ACTREC Biorepository and TMH-INTTR were analyzed for the effect of storage time on RNA quality. The RNA from tumor samples were isolated and analyzed by RIN, A260/280 ratio, and Ct value to establish inter-relationships. Around 50% samples had a RIN of ≥ 6.9 and A260/280 ≤ 2.04; 27% had a RIN ≥ 5 and A260/280 ≤ 2.08, and remaining 23% displayed RIN < 5 and A260/280 > 2.08. However, the RNA quality has no association with the storage period of tissue samples. Moreover, all samples which had A260/280 ≤ 2.08 showed acceptable Ct values of 17-24. The data clearly suggests that the A260/280 ratio is able to predict RNA quality. To the best of our knowledge, this is the first Indian report analyzing the labile nucleic acid-RNA quality from different cancer tissue types cryopreserved for diverse time periods. In conclusion, RIN and A260/280 ratio can help in predicting the quality of RNA independently; however, both together provide better assurance for further downstream processing. [ABSTRACT FROM AUTHOR]

Highlights • Ethanol stimulated expression of LeACS2 and LeACS4. • Ethanol treatment might induce genes encoding ripening-specific transcription factor. • Expression of RIN -dependent ripening-related genes was inhibited by ethanol. Abstract Postharvest ethanol vapor treatment suppresses tomato fruit ripening. The aim of this study was to clarify the mechanism of suppression at the molecular level. Tomato (Solanum lycopersicum cv. 'Micro Tom') fruit harvested at mature green and breaker stages was continuously treated with ethanol using an ethanol pad at 20 °C in the dark. Ethanol treatment stimulated ethylene production and increased gene expression of LeACS2 and LeACS4 , which are related to ethylene-related ripening. The expression of genes encoding ripening-specific transcription factors acting upstream of ethylene was also induced, when the fruit was treated with ethanol. In the ethylene-dependent ripening process, ethanol inhibited the expression of RIN -dependent and ethylene-dependent ripening-related genes, suggesting that ethanol could inhibit some processes downstream of ethylene perception. In the ethylene-independent ripening process, expression of RIN -dependent and ethylene-independent ripening related genes was inhibited by ethanol, suggesting that ethanol could inhibit some processes downstream of RIN. Inhibition of each process by ethanol could be a mechanism by which ethanol inhibits ripening, although it stimulates ethylene production and factors upstream of the ripening process. [ABSTRACT FROM AUTHOR]

Growing ecological concerns has led governments to utilize mechanisms such as Renewable Identification Number (RIN) in promoting biofuels as an alternative for fossil fuels. In this paper, a pricing model in a decentralized three-player biofuel supply chain with RIN mechanism is proposed and the interaction among members is analyzed using Stackelberg game. The optimal selling price of biomass, bioethanol, and RIN are obtained by solving the proposed discrete mathematical program with equilibrium constraints (DC-MPEC) problem which is transformed into a solvable mixed integer quadratic programming (MIQP) model. Finally, a real case study in Iran is presented to show the features of the model. Sensitivity analyses are performed which lead to some managerial insights into the effect of price elasticity and government policies on profits. Moreover, an evolutionary game theory approach is applied on the case study to show the long-term behavior of the members in the proposed RIN-based pricing model. [ABSTRACT FROM AUTHOR]

Demodex is a type of parasitic mite which could cause serious dermatoses in 11 orders of mammals. However, due to the tiny body with thick chitin hard to be ruptured as well as the difficulty in obtaining a large number of mites, the quantity and quality of extracted RNA could hardly satisfied for transcriptome sequencing. This has hampered the research on functional genes and molecular pathogenesis of Demodex for a long time. To solve the problems above, the present study established a new RNA extraction method in combination Azanno method with liquid nitrogen grinding using 16 human and canine Demodex mite samples. The RNA quality detection results of Agilent 2100 Bioanalyzer showed that 8 of 16 RNA samples met the requirements for trace RNA-Seq, with RIN of 5.0–6.5 and RNA quantity of 1.1–16.0 ng. RNA quality was affected by grinding process and parasitic position of Demodex. Enough grinding number (≥2000) in moderate time (≤20 min) was significant for mites' complete rupture and RNA degradation prevention. D. brevis (100%, 3/3) parasitizing in human sebaceous glands had significantly higher RNA qualification rate than D. folliculorum (57.14%, 4/7) parasitizing in human hair follicles. Yet D. canis parasitizing in dog had lower RNA qualification rate (16.67%, 1/6) as mites were embedded in skin tissues and blood clots. It should be pointed out that microplate reader had defects with a lower RNA qualification rate of 6.25% (1/16) unmatched with 2100 Bioanalyzer, reminding that it could be only used as reference in RNA quality evaluation. Image 1 • Azanno method & liquid nitrogen grinding successfully extracted RNA from pure Demodex. • grinding process and mites' parasitic position mainly affected the quality of extracted RNA. • microplate reader could be used only as a reference in RNA quality evaluation. • 2100 Bioanalyzer should be the more reliable method to detect RNA quality for RNA-Seq. [ABSTRACT FROM AUTHOR]

Summary: Ethylene is the main hormone controlling climacteric fruit ripening; however, the mechanisms underlying the developmental transition leading to the initiation of the ripening process remain elusive, although the presumed role of active hormone interplay has often been postulated.To unravel the putative role of auxin in the unripe‐to‐ripe transition, we investigated the dynamics of auxin activity in tomato fruit and addressed the physiological significance of Sl‐SAUR69, previously identified as a RIN target gene, using reverse genetics approaches.Auxin signalling undergoes dramatic decline at the onset of ripening in wild‐type fruit, but not in the nonripening rin mutant. Sl‐SAUR69 exhibits reduced expression in rin and its up‐regulation results in premature initiation of ripening, whereas its down‐regulation extends the time to ripening. Overexpression of Sl‐SAUR69 reduces proton pump activity and polar auxin transport, and ectopic expression in Arabidopsis alters auxin transporter abundance, further arguing for its active role in the regulation of auxin transport.The data support a model in which Sl‐SAUR69 represses auxin transport, thus generating auxin minima, which results in enhanced ethylene sensitivity. This defines a regulation loop, fed by ethylene and auxin as the main hormonal signals and by RIN and Sl‐SAUR69 as modulators of the balance between the two hormones. [ABSTRACT FROM AUTHOR]