A Method for Physical Analysis of Recombination Intermediates in Saccharomyces cerevisiae.

Meiosis is a process through which diploid cells divide into haploid cells, thus promoting genetic diversity. This diversity arises from the formation of genetic crossovers (COs) that repair DNA double-strand breaks (DSBs), through homologous recombination (HR). Deficiencies in HR can lead to chromosomal abnormality resulting from chromosomal nondisjunction, and genetic disorders. Therefore, investigating the mechanisms underlying effective HR is crucial for reducing genome instability. Budding yeast serves as an ideal model for studying HR mechanisms due to its amenability to gene modifications and the ease of inducing synchronized meiosis to yield four spores. During meiosis, at the DNA level, programmed DSBs are repaired as COs or non-crossovers (NCOs) through structural alterations in the nascent D-loop, involving single-end invasions (SEIs) and double-Holliday junctions (dHJs). This repair occurs using homologous templates rather than sister templates. This protocol, using Southern blotting, allows for the analysis and monitoring of changes in DNA structures in the recombination process. One-dimensional (1D) gel electrophoresis is employed to detect DSBs, COs, and NCOs, while two-dimensional (2D) gel electrophoresis is utilized to identify joint molecules (JMs). Therefore, physical analysis is considered the most effective method for investigating the HR mechanism. Our protocol provides more comprehensive information than previous reports by introducing conditions for obtaining a greater number of cells from synchronized yeast and a method that can analyze not only meiotic/mitotic recombination but also mitotic replication.

Ligand Effect in 1-Octanethiol Passivation of InP/ZnSe/ZnS Quantum Dots-Evidence of Incomplete Surface Passivation during Synthesis.

The lack of anionic carboxylate ligands on the surface of InP/ZnSe/ZnS quantum dots (QDs), where zinc carboxylate ligands can be converted to carboxylic acid or carboxylate ligands via proton transfer by 1-octanethiol, is demonstrated. The as-synthesized QDs initially have an under-coordinated vacancy surface, which is passivated by solvent ligands such as ethanol and acetone. Upon exposure of 1-octanethiol to the QD surface, 1-octanethiol effectively induces the surface binding of anionic carboxylate ligands (derived from zinc carboxylate ligands) by proton transfer, which consequently exchanges ethanol and acetone ligands that bind on the incomplete QD surface. These systematic chemical analyses, such as thermogravimetric analysis-mass spectrometry and proton nuclear magnetic resonance spectroscopy, directly show the interplay of surface ligands, and it associates with QD light-emitting diodes (QD-LEDs). It is believed that this better understanding can lead to industrially feasible QD-LEDs.

Activation of galactose utilization by the addition of glucose for the fermentation of agar hydrolysate using Lactobacillus brevis ATCC 14869.

OBJECTIVE: To investigate the application of carbon catabolite repression (CCR) relaxed Lactobacillus brevis ATCC 14869 in the utilization of agar hydrolysate to produce bioethanol and lactic acid through fermentation. RESULTS: As a single carbon source, galactose was not metabolized by L. brevis. However, L. brevis consumed galactose simultaneous to glucose and ceased cell growth after depletion of glucose. For complete use of galactose from agar hydrolysis, glucose need to be periodically replenished into the growth medium. Overall, L. brevis successfully used agar hydrolysate and produced 17.2 g/L of ethanol and 31.9 g/L of lactic acid. The maximum specific cell growth rate on galactose and glucose mixture was the same with the glucose-only medium at 0.12 h-1. The molar product yields from glucose for lactic acid and ethanol were 1.02 and 0.95 respectively, equal to values obtained from the simultaneous utilization of glucose and galactose. CONCLUSION: In contribution to the ongoing efforts to utilize marine biomass, the relaxed CCR in Lactobacillus brevis ATCC 14869 was herein exploited to produce bioethanol and lactic acid from red seaweed hydrolysates.

Enhanced Electroluminescence via a Nanohybrid Material Consisting of Aromatic Ligand-Modified InP Quantum Dots and an Electron-Blocking Polymer as the Single Active Layer in Quantum Dot-LEDs.

Electron overcharge causes rapid luminescence quenching in the quantum dot (QD) emission layer in QD light-emitting diodes (QD-LEDs), resulting in low device performance. In this paper we describe the application of different aromatic thiol ligands and their influence on device performance as well as their behavior in combination with an electron blocking material (EBM). The three different ligands, 1-octanethiol (OcSH), thiophenol (TP), and phenylbutan-1-thiol (PBSH), were introduced on to InP/ZnSe/ZnS QDs referred to as QD-OcSH, QD-TP, and QD-PBSH. PBSH is in particular applied as a ligand to improve QD solubility and to enhance the charge transport properties synergistically with EBM probably via π-π interaction. We synthesized poly-[N,N-bis[4-(carbazolyl)phenyl]-4-vinylaniline] (PBCTA) and utilized it as an EBM to alleviate excess electrons in the active layer in QD-LEDs. The comparison of the three QD systems in an inverted device structure without the application of PBCTA as an EBM shows the highest efficiency for QD-PBSH. Moreover, when PBCTA is introduced as an EBM in the active layer in combination with QD-PBSH in a conventional device structure, the current efficiency shows a twofold increase compared to the reference device without EBM. These results strongly confirm the role of PBCTA as an EBM that effectively alleviates excess electrons in the active layer, leading to higher device efficiency.

Maternal exposure to polystyrene nanoplastics causes brain abnormalities in progeny.

As global plastic production continues to grow, microplastics released from a massive quantity of plastic wastes have become a critical environmental concern. These microplastic particles are found in a wide range of living organisms in a diverse array of ecosystems. In this study, we investigated the biological effects of polystyrene nanoplastic (PSNP) on development of the central nervous system using cultured neural stem cells (NSCs) and mice exposed to PSNP during developmental stages. Our study demonstrates that maternal administration of PSNP during gestation and lactating periods altered the functioning of NSCs, neural cell compositions, and brain histology in progeny. Similarly, PSNP-induced molecular and functional defects were also observed in cultured NSCs in vitro. Finally, we show that the abnormal brain development caused by exposure to high concentrations of PSNP results in neurophysiological and cognitive deficits in a gender-specific manner. Our data demonstrate the possibility that exposure to high amounts of PSNP may increase the risk of neurodevelopmental defects.

Development of methods for determining free fatty acid contents in red colored oils.

Buah merah oil and red palm oil are red colored and unrefined edible oils. Because of this color characteristic, measuring acid value by titration method can be uncertain and subjective, so more accurate and objective methods are needed. Gas chromatography-flame ionization detector (GC-FID) and high-performance liquid chromatography-evaporative light scattering detector (HPLC-ELSD) methods were developed to determine acid value in 3 buah merah oils and 1 red palm oil by measuring free fatty acid contents. The acid value was high in the order of titration > GC-FID > HPLC-ELSD in all samples. GC-FID method showed accurate and reliable results, whereas HPLC-ELSD showed rough data partly due to the non-linear standard curve and high limit of detection. Difference in acid value between titration method and GC-FID might be due to unrefined components that reacted with KOH titration solution. GC-FID can be used measuring free fatty acid contents in red colored oils. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-00964-2.

The synaptonemal complex central region modulates crossover pathways and feedback control of meiotic double-strand break formation.

The synaptonemal complex (SC) is a proteinaceous structure that mediates homolog engagement and genetic recombination during meiosis. In budding yeast, Zip-Mer-Msh (ZMM) proteins promote crossover (CO) formation and initiate SC formation. During SC elongation, the SUMOylated SC component Ecm11 and the Ecm11-interacting protein Gmc2 facilitate the polymerization of Zip1, an SC central region component. Through physical recombination, cytological, and genetic analyses, we found that ecm11 and gmc2 mutants exhibit chromosome-specific defects in meiotic recombination. CO frequencies on a short chromosome (chromosome III) were reduced, whereas CO and non-crossover frequencies on a long chromosome (chromosome VII) were elevated. Further, in ecm11 and gmc2 mutants, more double-strand breaks (DSBs) were formed on a long chromosome during late prophase I, implying that the Ecm11-Gmc2 (EG) complex is involved in the homeostatic regulation of DSB formation. The EG complex may participate in joint molecule (JM) processing and/or double-Holliday junction resolution for ZMM-dependent CO-designated recombination. Absence of the EG complex ameliorated the JM-processing defect in zmm mutants, suggesting a role for the EG complex in suppressing ZMM-independent recombination. Our results suggest that the SC central region functions as a compartment for sequestering recombination-associated proteins to regulate meiosis specificity during recombination.

Metal Sulfide Nanoparticle Synthesis with Ionic Liquids - State of the Art and Future Perspectives.

Metal sulfides are among the most promising materials for a wide variety of technologically relevant applications ranging from energy to environment and beyond. Incidentally, ionic liquids (ILs) have been among the top research subjects for the same applications and also for inorganic materials synthesis. As a result, the exploitation of the peculiar properties of ILs for metal sulfide synthesis could provide attractive new avenues for the generation of new, highly specific metal sulfides for numerous applications. This article therefore describes current developments in metal sulfide nanoparticle synthesis as exemplified by a number of highlight examples. Moreover, the article demonstrates how ILs have been used in metal sulfide synthesis and discusses the benefits of using ILs over more traditional approaches. Finally, the article demonstrates some technological challenges and how ILs could be used to further advance the production and specific property engineering of metal sulfide nanomaterials, again based on a number of selected examples.

Dioleylphosphatidylcholine increases the antioxidant properties of ascorbyl palmitate in bulk oils compared to other hydrophilic and lipophilic antioxidants.

Effects of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and moisture on the solubility of hydrophilic and lipophilic antioxidants were evaluated in medium-chain triacylglycerol (MCT) by 2,2-diphenyl-1-picrylhydrazyl (DPPH) reactivity. Next, we assessed the oxidative stability of antioxidant-containing corn oil depending on the presence of DOPC. The critical micelle concentration (CMC) of DOPC decreased when the moisture content was increased from 300 to 495 mg/kg oil and gradually increased when the moisture was further increased to 2122 mg/kg oil. As the DOPC concentration increased, the DPPH reactivity of ascorbyl palmitate in the control MCT increased by 10.23-fold, whereas that of the ascorbic acid and α-tocopherol was slightly affected both by the DOPC and moisture content. Presence of DOPC significantly increased the oxidative stability of ascorbyl palmitate-containing corn oil (p < 0.05), whereas these synergistic antioxidant effects were not observed in ascorbic acid-or α-tocopherol-containing corn oil. In conclusion, DOPC displays a synergistic antioxidant effect with ascorbyl palmitate in bulk oil.

Effects of Ultra-high doserate FLASH Irradiation on the Tumor Microenvironment in Lewis Lung Carcinoma: Role of Myosin Light Chain.

PURPOSE: To investigate whether the vascular collapse in tumors by conventional dose rate (CONV) irradiation (IR) would also occur by the ultra-high dose rate FLASH IR. METHODS AND MATERIALS: Lewis lung carcinoma (LLC) cells were subcutaneously implanted in mice. This was followed by CONV or FLASH IR at 15 Gy. Tumors were harvested at 6 or 48 hours after IR and stained for CD31, phosphorylated myosin light chain (p-MLC), γH2AX (a surrogate marker for DNA double strand break), intracellular reactive oxygen species (ROS), or immune cells such as myeloid and CD8α T cells. Cell lines were irradiated with CONV IR for Western blot analyses. ML-7 was intraperitoneally administered daily to LLC-bearing mice for 7 days before 15 Gy CONV IR. Tumors were similarly harvested and analyzed. RESULTS: By immunostaining, we observed that CONV IR at 6 hours resulted in constricted vessel morphology, increased expression of p-MLC, and much higher numbers of γH2AX-positive cells in tumors, which were not observed with FLASH IR. Mechanistically, MLC activation by ROS is unlikely, because FLASH IR produced significantly more ROS than CONV IR in tumors. In vitro studies demonstrated that ML-7, an inhibitor of MLC kinase, abrogated IR-induced γH2AX formation and disappearance kinetics. Lastly, we observed that CONV IR when combined with ML-7 produced some effects similar to FLASH IR, including reduction in the vasculature collapse, fewer γH2AX-positive cells, and increased immune cell influx to the tumors. CONCLUSIONS: FLASH IR produced novel changes in the tumor microenvironment that were not observed with CONV IR. We believe that MLC activation in tumors may be responsible for some of the microenvironmental changes differentially regulated between CONV and FLASH IR.

Development of a 3D scanning method to discriminate blocks of Octopus minor with surplus water gain.

A 3D scanning method was developed to differentiate Octopus minor blocks which had surplus water to increase weight of O. minor. Effects of soaking time (0.5, 1 and 3 h) and apparent density of O. minor were determined using the number of O. minor in a block (4, 5, 6, and 7). A 0.5, 1, and 3 h soaking time increased O. minor weight by 11.85, 16.02, and 24.53%, respectively. Apparent density of non-weight gained O. minor blocks was significantly higher than those of 3 h soaked samples (p < 0.05). A 3D scanning method had limited ability to differentiate 1 h soaked and non-soaked samples, whereas it had high potential to discriminate 3 h soaked samples. Blind test using 25 blocks of O. minor showed that 3D scanning method evaluated 88% of prediction percentage. The total time of 3D scanning took <30 min for one block with a relatively high precision.

Mec1 Modulates Interhomolog Crossover and Interplays with Tel1 at Post Double-Strand Break Stages.

During meiosis I, programmed DNA double-strand breaks (DSBs) occur to promote chromosome pairing and recombination between homologs. In Saccharomyces cerevisiae, Mec1 and Tel1, the orthologs of human ATR and ATM, respectively, regulate events upstream of the cell cycle checkpoint to initiate DNA repair. Tel1ATM and Mec1ATR are required for phosphorylating various meiotic proteins during recombination. This study aimed to investigate the role of Tel1ATM and Mec1ATR in meiotic prophase via physical analysis of recombination. Tel1ATM cooperated with Mec1ATR to mediate DSB-to-single end invasion transition, but negatively regulated DSB formation. Furthermore, Mec1ATR was required for the formation of interhomolog joint molecules from early prophase, thus establishing a recombination partner choice. Moreover, Mec1ATR specifically promoted crossover-fated DSB repair. Together, these results suggest that Tel1ATM and Mec1ATR function redundantly or independently in all post-DSB stages.

Comparative Whole Cell Proteomics of Listeria monocytogenes at Different Growth Temperatures.

Listeria monocytogenes is a gram-positive, facultative anaerobe food pathogen responsible for the listeriosis that mostly occurs during the low-temperature storage of a cold cut or dairy products. To understand the systemic response to a wide range of growth temperatures, L. monocytogenes were cultivated at a different temperature from 10°C to 42°C, then whole cell proteomic analysis has been performed both exponential and stationary cells. The specific growth rate increased proportionally with the increase in growth temperature. The maximum growth rate was observed at 37°C and was maintained at 42°C. Global protein expression profiles mainly depended on the growth temperatures showing similar clusters between exponential and stationary phases. Expressed proteins were categorized by their belonging metabolic systems and then, evaluated the change of expression level in regard to the growth temperature and stages. DnaK, GroEL, GroES, GrpE, and CspB, which were the heat&cold shock response proteins, increased their expression with increasing the growth temperatures. In particular, GroES and CspB were expressed more than 100-fold than at low temperatures during the exponential phase. Meanwhile, CspL, another cold shock protein, overexpressed at a low temperature then exponentially decreased its expression to 65-folds. Chemotaxis protein CheV and flagella proteins were highly expressed at low temperatures and stationary phases. Housekeeping proteins maintained their expression levels constant regardless of growth temperature or growth phases. Most of the growth related proteins, which include central carbon catabolic enzymes, were highly expressed at 30°C then decreased sharply at high growth temperatures.

Oxidative Stability in Oil-in-Water Emulsions with Quercetin or Rutin Under Iron Catalysis or Riboflavin Photosensitization.

The effects of quercetin and rutin on the oxidative stability of oil-in-water (O/W) emulsions were tested under riboflavin (RF) photosensitization in the presence or absence of FeCl2 . The degree of oxidation in O/W emulsions was determined by headspace oxygen content, conjugated dienes, and lipid hydroperoxides. Quercetin chelated more metal than did rutin in iron catalyzed O/W emulsions. Generally, 0.1 mM quercetin and rutin was oxidative while 0.5 and 1.0 mM quercetin and rutin was antioxidative in O/W emulsions under RF photosensitization. Depending on the analysis method, the antioxidants had different strengths. The antioxidative or oxidative properties of quercetin and rutin vary in O/W emulsions and depend the quercetin and rutin concentrations and oxidative forces like transition metals, RF photosensitization, or a combination thereof.

Radiation-induced immune responses: mechanisms and therapeutic perspectives.

Recent advancement in the radiotherapy technology has allowed conformal delivery of high doses of ionizing radiation precisely to the tumors while sparing large volume of the normal tissues, which have led to better clinical responses. Despite this technological advancement many advanced tumors often recur and they do so within the previously irradiated regions. How could tumors recur after receiving such high ablative doses of radiation? In this review, we outlined how radiation can elicit anti-tumor responses by introducing some of the cytokines that can be induced by ionizing radiation. We then discuss how tumor hypoxia, a major limiting factor responsible for failure of radiotherapy, may also negatively impact the anti-tumor responses. In addition, we highlight how there may be other populations of immune cells including regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and tumor-associated macrophages (TAMs) that can be recruited to tumors interfering with the anti-tumor immunity. Finally, the impact of irradiation on tumor hypoxia and the immune responses according to different radiotherapy regimen is also delineated. It is indeed an exciting time to see that radiotherapy is being combined with immunotherapy in the clinic and we hope that this review can add an excitement to the field.

Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles.

There are fundamental limitations in inferring the functional interaction structure of a gene (regulatory) network only from sequence information such as binding motifs. To overcome such limitations, various approaches have been developed to infer the functional interaction structure from expression profiles. However, most of them have not been so successful due to the experimental limitations and computational complexity. Hence, there is a pressing need to develop a simple but effective methodology that can systematically identify the functional interaction structure of a gene network from time-series expression profiles. In particular, we need to take into account the different time delay effects in gene regulation since they are ubiquitously present. We have considered a new experiment that measures the overall expression changes after a perturbation on a specific gene. Based on this experiment, we have proposed a new inference method that can take account of the time delay induced while the perturbation affects its primary target genes. Specifically, we have developed an algebraic equation from which we can identify the subnetwork structure around the perturbed gene. We have also analyzed the influence of time delay on the inferred network structure. The proposed method is particularly useful for identification of a gene network with small variations in the time delay of gene regulation.

Integrative analysis of time course microarray data and DNA sequence data via log-linear models for identifying dynamic transcriptional regulatory networks.

Since eukaryotic transcription is regulated by sets of Transcription Factors (TFs) having various transcriptional time delays, identification of temporal combinations of activated TFs is important to reconstruct Transcriptional Regulatory Networks (TRNs). Our methods combine time course microarray data, information on physical binding between the TFs and their targets and the regulatory sequences of genes using a log-linear model to reconstruct dynamic functional TRNs of the yeast cell cycle and human apoptosis. In conclusion, our results suggest that the proposed dynamic motif search method is more effective in reconstructing TRNs than the static motif search method.

Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress.

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been studied as an extremophile that has successfully adapted to marginal land with the harshest environment for terrestrial plants. However, limited genetic research has focused on this species due to the lack of genomic resources. Here, we present the first de novo assembly of its transcriptome by massive parallel sequencing and its expression profile using D. antarctica grown under various stress conditions. Total sequence reads generated by pyrosequencing were assembled into 60,765 unigenes (28,177 contigs and 32,588 singletons). A total of 29,173 unique protein-coding genes were identified based on sequence similarities to known proteins. The combined results from all three stress conditions indicated differential expression of 3,110 genes. Quantitative reverse transcription polymerase chain reaction showed that several well-known stress-responsive genes encoding late embryogenesis abundant protein, dehydrin 1, and ice recrystallization inhibition protein were induced dramatically and that genes encoding U-box-domain-containing protein, electron transfer flavoprotein-ubiquinone, and F-box-containing protein were induced by abiotic stressors in a manner conserved with other plant species. We identified more than 2,000 simple sequence repeats that can be developed as functional molecular markers. This dataset is the most comprehensive transcriptome resource currently available for D. antarctica and is therefore expected to be an important foundation for future genetic studies of grasses and extremophiles.

A pathway-based classification of breast cancer integrating data on differentially expressed genes, copy number variations and microRNA target genes.

Breast cancer is a clinically heterogeneous disease characterized by distinct molecular aberrations. Understanding the heterogeneity and identifying subgroups of breast cancer are essential to improving diagnoses and predicting therapeutic responses. In this paper, we propose a classification scheme for breast cancer which integrates data on differentially expressed genes (DEGs), copy number variations (CNVs) and microRNAs (miRNAs)-regulated mRNAs. Pathway information based on the estimation of molecular pathway activity is also applied as a postprocessor to optimize the classifier. A total of 250 malignant breast tumors were analyzed by k-means clustering based on the patterns of the expression profiles of 215 intrinsic genes, and the classification performances were compared with existing breast cancer classifiers including the BluePrint and the 625-gene classifier. We show that a classification scheme which incorporates pathway information with various genetic variations achieves better performance than classifiers based on the expression levels of individual genes, and propose that the identified signature serves as a basic tool for identifying rational therapeutic opportunities for breast cancer patients.

p53 and microRNA-34 are suppressors of canonical Wnt signaling.

Although loss of p53 function and activation of canonical Wnt signaling cascades are frequently coupled in cancer, the links between these two pathways remain unclear. We report that p53 transactivated microRNA-34 (miR-34), which consequently suppressed the transcriptional activity of ß-catenin-T cell factor and lymphoid enhancer factor (TCF/LEF) complexes by targeting the untranslated regions (UTRs) of a set of conserved targets in a network of genes encoding elements of the Wnt pathway. Loss of p53 function increased canonical Wnt signaling by alleviating miR-34-specific interactions with target UTRs, and miR-34 depletion relieved p53-mediated Wnt repression. Gene expression signatures reflecting the status of ß-catenin-TCF/LEF transcriptional activity in breast cancer and pediatric neuroblastoma patients were correlated with p53 and miR-34 functional status. Loss of p53 or miR-34 contributed to neoplastic progression by triggering the Wnt-dependent, tissue-invasive activity of colorectal cancer cells. Further, during development, miR-34 interactions with the ß-catenin UTR affected Xenopus body axis polarity and the expression of Wnt-dependent patterning genes. These data provide insight into the mechanisms by which a p53-miR-34 network restrains canonical Wnt signaling cascades in developing organisms and human cancer.