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Gene is a factor encoding genetic information and the basic unit of inheritance. Gene expression is a phenomenon consisting of two complex stages of transcription and translation. In this study, the yeast cell of Saccharomyces cerevisiae evolution is investigated due to the importance of the gene expression phenomenon. To clarify the accuracy of the obtained results, we have used experimental data on the Saccharomyces cerevisiae yeast cell from the gene bank. We are using chaos theory to study gene expression due to the nonlinear dynamics of the phenomenon. The obtained results predict that, by increasing the rate of degradation in the messenger arena to 0.03, we have reached the threshold value for the gene expression phenomenon. Also, we have recognized that increased transcription is associated with an increased mRNA degradation rate. The optimal values of transcription delay rate (18.2 min) and protein degradation rate (0.03) were obtained. There was a good agreement between the experimental and theoretical results.

The article announces the winners of Development's Outstanding Paper Prize for papers published in 2023. The winning papers focus on developmental and stem cell biology. One paper demonstrates the potential of genome engineering techniques and pharmacological upregulation of the Wnt signaling pathway in treating frizzled 2-associated congenital malformations in mouse models. Another paper explores how Frizzled2 receives WntA signaling during butterfly wing pattern formation, providing insights into the complexity and evolution of signaling pathways. The article also mentions a study on the development of primordial germ cell-like cells using stem cell technologies. Additionally, the article discusses a study on the molecular functioning of WntA in butterfly wing color patterning, which involved collaboration between international teams and faced challenges in rearing and injecting butterflies in the lab. The researchers plan to further investigate butterfly color patterns. [Extracted from the article]

A high mortality rate was found in cancer patients with distant metastasis. Development of targeted drugs for effectively inhibiting cancer metastasis is the key for increasing therapeutic success. In the current study, a folding paper system was developed to mimic a tumor–vascular interface for the study of long-distance cell migration. Correlation between the cell migration distance and metastasis-associated gene was successfully analyzed by disassembling the stacked paper construct. The result revealed that the migration distance and number of migrated cells were highly correlated to cell characteristics. Moreover, immunocytochemistry was directly conducted on the paper layer to study the signaling pathway. Kelch-like and protein tyrosine phosphatase families were examined and the PTPN13 gene was shown to regulate long-distance cell migration. By analyzing the phosphorylated mTOR, the PTPN13 gene was further confirmed to be a tumor suppressor gene that inhibits long-distance cell migration. The folding paper system provides an alternative approach for long-distance cell migration. Metastasis-associated gene expression can be analyzed to potentially develop targeted drugs for cancer metastasis inhibition. [ABSTRACT FROM AUTHOR]

This article features an interview with Jingjing Sun and Angelike Stathopoulos, who conducted a study on the collective migration of caudal visceral mesoderm (CVM) cells in Drosophila embryos. They discovered that cell division coordinates two gene expression programs in migrating CVM cells. The researchers discuss their scientific backgrounds and the questions they are trying to answer in their lab. They also highlight the importance of the Drosophila system for their research. The study's key findings include the identification of two groups of genes that regulate the behaviors of CVM cells during migration, and the role of cell division in controlling gene expression programs. The researchers also discuss their motivations and future directions for their research. [Extracted from the article]

The paper mulberry is a commonly found tree species with a long history of cultivation. It also serves as a crucial case study for understanding how woody plants adapt to low temperatures. Under cold treatment, we observed a substantial number of alternative splicing (AS) genes, showcasing the intricate landscape of AS events. We have detected all seven types of AS events, with the alternative 3′ splice site (A3) having the most. We observed that many genes that underwent differential AS were significantly enriched in starch and sucrose metabolism and circadian rhythm pathways. Moreover, a considerable proportion of differentially spliced genes (DSGs) also showed differential expression, with 20.38% and 25.65% under 12 h and 24 h cold treatments, respectively. This suggests a coordinated regulation between gene AS and expression, playing a pivotal role in the paper mulberry's adaptation to cold stress. We further investigated the regulatory mechanisms of AS, identifying 41 serine/arginine-rich (SR) splicing factors, among which 11 showed differential expression under cold treatment, while 29 underwent alternative splicing. Additionally, genes undergoing AS displayed significantly higher DNA methylation levels under cold stress, while normal splicing (non-AS) genes exhibited relatively lower methylation levels. These findings suggest that methylation may play an important role in governing gene AS. Finally, our research will provide useful information on the role of AS in the cold acclimation tolerance of the paper mulberry. [ABSTRACT FROM AUTHOR]

This article is an interview with Charlotte Manser and Ruben Perez-Carrasco, discussing their recent paper on the molecular basis of developmental timing. The authors developed a mathematical framework to explore the tempo of development and identify molecular mechanisms that regulate it. They studied gene expression orbits and used mathematical methods to define function and tempo in a quantitative way. The paper aims to reach experimentalists in the developmental biology community and is published in the journal Development. Manser and Perez-Carrasco plan to continue exploring the role of tempo in different developmental systems and are excited about potential applications in synthetic biology and immunology. Outside of their research, they enjoy playing Dungeons & Dragons and have a shared love for music. [Extracted from the article]

Abstract Background Heavy metal contamination is becoming a limitation to the utilization of soil and the distribution of vegetation. In particular, cadmium (Cd) pollution has had a serious impact on the food chain. Broussonetia papyrifera is a widely distributed pioneer tree species of heavy metal contaminated areas with important economic value. However, little is known about the genomic background of the Cd-tolerance mechanism in B. papyrifera. Results The CdCl 2 responsive physiology was evaluated and proved to be involved in antioxidase activity and active oxygen species (ROS) accumulation. The leaf and root transcriptomes derived from B. papyrifera grown under normal and CdCl 2 stress conditions were systematically investigated using the Illumina HiSeq method. A total of 180,678,660 bp (27.1 GB) clean reads were assembled into 589,487 high-quality unigenes, of which 256,025 (43.43% of the total) and 250,251 (42.45% of the total) were aligned in Gene Ontology (GO) and Protein family (Pfam), respectively. A total of 24,414 differentially expressed genes (DEGs) were GO-annotated into 53, 23, 55, and 60 terms from the transcriptomes of root and leaf tissues under Cd stress and control conditions. A total of 117,547 Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)-annotated DEGs were enriched in at least 47 KEGG pathway terms among the four comparisons. Many genes encoding important transcription factors (e.g., auxin/indole-3-acetic acid (AUX/IAA), basic helix-loop-helix (bHLH), DNA-binding one zinc finger (Dof), and MYB) and proteins involved in plant-pathogen interactions, phenylpropanoid biosynthesis, plant hormone signal transduction, oxidative phosphorylation, carbon fixation, peroxisomes, flavonoid biosynthesis, and glutathione metabolism, among others, were substantially upregulated under CdCl 2 stress. Conclusions These genes represent important candidates for studying Cd-response mechanisms and molecular biology of B. papyrifera and related species. Our findings provide a genomic sequence resource for functional genetic assignments in B. papyrifera , which will help elucidate the molecular mechanisms of its Cd-stress responses and facilitate the bioremediation of heavy metal contaminated areas via breeding of new stress-tolerant cultivars. Graphical abstract fx1 Highlights • Broussonetia papyrifera respond to Cd stress involving in reactive oxygen species and antioxidant enzyme metabolic pathway. • Abundant important Cd response related genes and regulation pathways that involving in ABA and auxin signal were identified. • The gene resource of B. papyrifera will help elucidate the molecular mechanisms of Cd-stress responses. [ABSTRACT FROM AUTHOR]

Invasive paper wasps such as Polistes dominula are a major pest and problem for biodiversity around the globe. Safe and highly targeted methods for the control of these and other social wasp populations are needed. We attempted to identify potentially-lethal gene targets that could be used on adult paper wasps in a gene silencing or RNA interference (RNAi) approach. Double-stranded RNA (dsRNA) was designed to target genes for which silencing has proven lethal in other insects. dsRNA was provided either orally to foragers or directly injected into the wasps. We also provided the dsRNA unprotected or protected from degradation by gut nucleases in two different forms (lipofectamine and carbon quantum dots). The effects of oral delivery of 22 different gene targets to forager wasps was evaluated. The expression of five different genes was successfully reduced following dsRNA ingestion or injection. These gene targets included the FACT complex subunit spt16 (DRE4) and RNA-binding protein fusilli (FUSILLI), both of which have been previously shown to have potential as lethal targets for pest control in other insects. However, we found no evidence of significant increases in adult wasp mortality following ingestion or injection of dsRNA for these genes when compared with control treatments in our experiments. The methods we used to protect the dsRNA from digestive degradation altered gene expression but similarly did not influence wasp mortality. Our results indicate that while many of the same gene targets can be silenced and induce mortality in other insects, dsRNA and RNAi approaches may not be useful for paper wasp control. [ABSTRACT FROM AUTHOR]

Background: The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging when the information itself resides beyond titles or abstracts. For emerging science, with a limited set of known papers of interest and an incomplete information model, this is of pressing concern. A timely example in retrospect is the identification of immune signatures (coherent sets of biomarkers) driving differential SARS-CoV-2 infection outcomes. Implementation: We built a classifier to identify papers containing domain-specific information from the document embeddings of the title and abstract. To train this classifier with limited data, we developed an iterative process leveraging pre-trained SPECTER document embeddings, SVM classifiers and web-enabled expert review to iteratively augment the training set. This training set was then used to create a classifier to identify papers containing domain-specific information. Finally, information was extracted from these papers through a semi-automated system that directly solicited the paper authors to respond via a web-based form. Results: We demonstrate a classifier that retrieves papers with human COVID-19 immune signatures with a positive predictive value of 86%. The type of immune signature (e.g., gene expression vs. other types of profiling) was also identified with a positive predictive value of 74%. Semi-automated queries to the corresponding authors of these publications requesting signature information achieved a 31% response rate. Conclusions: Our results demonstrate the efficacy of using a SVM classifier with document embeddings of the title and abstract, to retrieve papers with domain-specific information, even when that information is rarely present in the abstract. Targeted author engagement based on classifier predictions offers a promising pathway to build a semi-structured representation of such information. Through this approach, partially automated literature mining can help rapidly create semi-structured knowledge repositories for automatic analysis of emerging health threats. [ABSTRACT FROM AUTHOR]

Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners. [ABSTRACT FROM AUTHOR]

They describe the structure of the MRN Complex and its function in double-strand break (DSB) repair and analyze the different germline alterations of the MRN complex genes in autosomal recessive syndromes, as well as the association between heterozygous germline alterations in these genes and cancer predisposition. In the rapidly evolving landscape of molecular genetics and genomics, this Special Issue brings together a collection of insightful review articles that delve into the forefront of scientific exploration. The authors also propose a possible explanation of the discrepancies in the published results of the effects of the OXTR gene polymorphisms and methylation on different diseases [[2]]. [Extracted from the article]

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes ( NADH dehydrogenase ( NADHdh) and retinoid and fatty acid binding protein ( RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field. [ABSTRACT FROM AUTHOR]

Paper mulberry vein banding virus (PMVBV), a member of the genus Badnavirus in the family Caulimoviridae, infects paper mulberry (Broussonetia papyrifera), a dicotyledonous plant. Putative promoter regions in the PMVBV genome were tested using recombinant plant expression vectors, revealing that the promoter activity of three genome fragments was about 1.5-fold higher than that of the 35S promoter of cauliflower mosaic virus in Nicotiana benthamiana. In transformed transgenic Arabidopsis thaliana plants, these promoter constructs showed constitutive expression. Based on the activity and gene expression patterns of these three promoter constructs, a fragment of 384 bp (named PmVP) was deduced to contain the full-length promoter of the PMVBV genome. The results suggest that the PMVBV-derived promoter can be used for the constitutive expression of transgenes in dicotyledonous plants. [ABSTRACT FROM AUTHOR]

Few animals are known to individually recognize conspecifics, i.e. learn and recall unique individuals during subsequent encounters, and nearly all are social vertebrates. Remarkably, the social paper wasp Polistes fuscatus has recently been discovered to possess this ability, which is useful for remembering identities during competitive social interactions. We analyzed brain gene expression in staged encounters between pairs of individuals to explore potential mechanisms underlying wasps' ability to recall familiar individuals using real-time qRT-PCR. We identified four candidate genes ( IP3K, IP3R, Nckx30C and Su(var)2- 10) that were down-regulated in the presence of familiar individuals compared to single wasps and pairs of wasps meeting for the first time. These candidate genes are related to calcium signaling, therefore, we treated wasps with lithium chloride, a pharmacological agent that inhibits calcium signaling in neurons. This treatment decreased aggression in paper wasps, but did not affect expression of genes related to calcium signaling. The results suggest calcium signaling differences may be related to individual memory recall in wasps, and we present four promising candidate genes for future study. These data suggest genes associated with dominance behavior may be co-opted for individual recognition, but further work is needed to establish a causal association with the behavior. [ABSTRACT FROM AUTHOR]

Gene expression responses of paper birch (Betula papyrifera) leaves to elevated concentrations of CO2 and O3 were studied with microarray analyses from three time points during the summer of 2004 at Aspen FACE. Microarray data were analyzed with clustering techniques, self-organizing maps, K-means clustering and Sammon''s mappings, to detect similar gene expression patterns within sampling times and treatments. Most of the alterations in gene expression were caused by O3, alone or in combination with CO2. O3 induced defensive reactions to oxidative stress and earlier leaf senescence, seen as decreased expression of photosynthesis- and carbon fixation-related genes, and increased expression of senescence-associated genes. The effects of elevated CO2 reflected surplus of carbon that was directed to synthesis of secondary compounds. The combined CO2 +O3 treatment resulted in differential gene expression than with individual gas treatments or in changes similar to O3 treatment, indicating that CO2 cannot totally alleviate the harmful effects of O3. [Copyright &y& Elsevier]

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. [ABSTRACT FROM AUTHOR]

Background In social groups, dominant individuals may socially inhibit reproduction of subordinates using aggressive interactions or, in the case of highly eusocial insects, pheromonal communication. It has been hypothesized these two modes of reproductive inhibition utilize conserved pathways. Here, we use a comparative framework to investigate the chemical and genomic underpinnings of reproductive dominance in the primitively eusocial wasp Polistes metricus. Our goals were to first characterize transcriptomic and chemical correlates of reproductive dominance and second, to test whether dominance-associated mechanisms in paper wasps overlapped with aggression or pheromone-related gene expression patterns in other species. To explore whether conserved molecular pathways relate to dominance, we compared wasp transcriptomic data to previous studies of gene expression associated with pheromonal communication and queen-worker differences in honey bees, and aggressive behavior in bees, Drosophila, and mice. Results By examining dominant and subordinate females from queen and worker castes in early and late season colonies, we found that cuticular hydrocarbon profiles and genome-wide patterns of brain gene expression were primarily associated with season/social environment rather than dominance status. In contrast, gene expression patterns in the ovaries were associated primarily with caste and ovary activation. Comparative analyses suggest genes identified as differentially expressed in wasp brains are not related to queen pheromonal communication or caste in bees, but were significantly more likely to be associated with aggression in other insects (bees, flies), and even a mammal (mice). Conclusions This study provides the first comprehensive chemical and molecular analysis of reproductive dominance in paper wasps. We found little evidence for a chemical basis for reproductive dominance in P. metricus, and our transcriptomic analyses suggest that different pathways regulate dominance in paper wasps and pheromone response in bees. Furthermore, there was a substantial impact of season/social environment on gene expression patterns, indicating the important role of external cues in shaping the molecular processes regulating behavior. Interestingly, genes associated with dominance in wasps were also associated with aggressive behavior in bees, solitary insects and mammals. Thus, genes involved in social regulation of reproduction in Polistes may have conserved functions associated with aggression in insects and other taxa. [ABSTRACT FROM AUTHOR]

Increasing cellulase production in cellulolytic fungus Trichoderma reesei is of interest for biofuels and biorefineries. Previous studies indicated that secreted protein was occasionally accumulated in vacuoles; this phenomenon has also been reported in T. reesei. Therefore, alleviating vacuolar transport seems to be a promising strategy for improving cellulase production in T. reesei. Herein, we found that knockout of vps10, vps13, and vps21, among 11 vacuolar protein sorting factors, improved cellulase production in T. reesei. The filter paper activity in Δvps10, Δvps13, and Δvps21 increased by 1.28-, 2.45-, and 2.11-fold than that of the parent strain. Moreover, the β-glucosidase activity in Δvps13 and Δvps21 increased by 3.22- and 3.56-fold after 6 days of fermentation. Furthermore, we also found that the vacuolar trafficking towards vacuoles was partially impaired in three knockout mutants, and disruption of vps13 alleviated the autophagy process. These results indicated that alleviated transport and degradation towards vacuole in Δvps10, Δvps13, and Δvps21 might improve cellulase production. Of note, the expression of cellulase genes in Δvps13 and Δvps21 was dramatically increased in the late induction phase compared to the parent. These results suggested that Vps13 and Vps21 might influence the cellulase production at transcription level. And further transcriptome analysis indicated that increased cellulase gene expression might be attributed to the differential expression of sugar transporters. Our study unravels the effect of alleviating vacuolar transport through knockout vps10, vps13, and vps21 for efficient cellulase secretion, providing new clues for higher cellulase production in T. reesei. Key points: • Disruption of vps10, vps13 or vps21 improves cellulase production • Vacuolar transport is impaired in three vps KO mutants • Deletion of vps13 or vps21 increases the transcript of cellulase genes in late stage [ABSTRACT FROM AUTHOR]

Operational tolerance after liver transplantation has been described in around 20% of the recipients. These patients are able to maintain a normal graft function in the absence of immunosuppressive drugs, thus being free of adverse effects that are common and frequently severe. Here we present a well-documented case of operational tolerance after liver transplantation and discuss current concepts on this topic with emphasis on recent findings that will potentially allow for identifying graft-tolerant patients.

Why workers forfeit direct reproduction is a crucial question in eusocial evolution. Worker reproduction provides an excellent opportunity to understand the mechanism of kin conflict resolution between the queen and workers. We evaluated behavioral and physiological differences among females in the paper wasp Polistes chinensis antennalis to examine why some workers reproduce under queenright conditions. Reproductive workers were old and foraged less early in the season; their cuticular hydrocarbon (CHC) profiles overlapped with those of queens but were significantly different. The distinct CHC profile of the eggs of the queen likely represented a cue for policing against those by workers. Juvenile hormone (JH) and dopamine seemed to be associated with gonadotropic function, and the JH level of reproductive workers was similar to that of the queen. The high JH level of reproductive workers likely facilitated their reproduction even under queenright conditions. Gene expression levels of the queen and reproductive workers differed only in vitellogenin. These results suggest that worker reproduction is facilitated by an increase in JH level; however, CHC is not a fertility-linked signal, but a queen-linked signal; consequently, reproductive workers without a queen-linked signal might be allowed to stay within the colony. [ABSTRACT FROM AUTHOR]

The gut microbiota is recognized as having major impact in health and disease. Sample storage is an important aspect to obtain reliable results. Mostly recommended is immediate freezing, however, this is not always feasible. Faecal occult blood test (FOBT) papers are an appealing solution in such situations, and most studies find these to be applicable, showing no major changes within 7 days storage at room temperature (RT). As fieldwork often requires RT storage for longer periods, evaluation of this is warranted. We performed 16S rRNA gene sequencing of 19 paired faecal samples immediately frozen or kept five weeks and five months at RT on FOBT papers. Alpha-diversity evaluation revealed no effect of FOBT storage, and evaluation of beta-diversity showed that host explained 65% of community variation, while storage method explained 5%. Evaluation of community dispersion and the Firmicutes/Bacteroidetes ratio revealed a larger effect of storage time for fresh-frozen samples. Single taxa evaluation (order-to-genus level) showed significant alterations of four (of 37) genera after five weeks and five genera after five months. When comparing the two timepoints, alterations were only detectable for fresh-frozen samples. Our findings reveal that long term storage on FOBT papers is an applicable approach for microbiota research. [ABSTRACT FROM AUTHOR]

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. [ABSTRACT FROM AUTHOR]

Comparative sociogenomics has the potential to provide important insights into how social behaviour evolved. We examined brain gene expression profiles of the primitively eusocial wasp Polistes metricus and compared the results with a growing base of brain gene expression information for the advanced eusocial honeybee, Apis mellifera. We studied four female wasp groups that show variation in foraging/provisioning behaviour and reproductive status, using our newly developed microarray representing approximately 3248 P. metricus genes based on sequences generated from high-throughput pyrosequencing. We found differences in the expression of approximately 389 genes across the four groups. Pathways known from Drosophila melanogaster to be related to lipid metabolism, heat and stress response, and various forms of solitary behaviour were associated with behavioural differences among wasps. Forty-five per cent of differentially expressed transcripts showed significant associations with foraging/provisioning status, and 14 per cent with reproductive status. By comparing these two gene lists with lists of genes previously shown to be differentially expressed in association with honeybee division of labour, we found a significant overlap of genes associated with foraging/provisioning, but not reproduction, across the two species. These results suggest common molecular roots for foraging division of labour in two independently evolved social insect species and the possibility of more lineage-specific roots of reproductive behaviour. We explore the implications of these findings for the idea that there is a conserved ‘genetic toolkit’ for division of labour across multiple lineages. [ABSTRACT FROM AUTHOR]

Biosensors have emerged as a valuable tool with high specificity and sensitivity for fast and reliable detection of hazardous substances in drinking water. Numerous substances have been addressed using synthetic biology approaches. However, many proposed biosensors are based on living, genetically modified organisms and are therefore limited in shelf life, usability and biosafety. We addressed these issues by the construction of an extensible, cell-free biosensor. Storage is possible through freeze drying on paper. Following the addition of an aqueous sample, a highly efficient cell-free protein synthesis (CFPS) reaction is initiated. Specific allosteric transcription factors modulate the expression of ‘superfolder’ green fluorescent protein (sfGFP) depending on the presence of the substance of interest. The resulting fluorescence intensities are analyzed with a conventional smartphone accompanied by simple and cheap light filters. An ordinary differential equitation (ODE) model of the biosensors was developed, which enabled prediction and optimization of performance. With an optimized cell-free biosensor based on the Shigella flexneri MerR transcriptional activator, detection of 6 μg/L Hg(II) ions in water was achieved. Furthermore, a completely new biosensor for the detection of gamma-hydroxybutyrate (GHB), a substance used as date-rape drug, was established by employing the naturally occurring transcriptional repressor BlcR from Agrobacterium tumefaciens. [ABSTRACT FROM AUTHOR]

The article cites a research study that examines the role of MiR- Par3L axis in breast cancer progression. It examined normal tissues and Par3L expressions in breast cancer tissues and cells. Par3L was found to be frequently down-regulated in human breast cancer cells and tissues and Par3L low-expression was associated with aggressive clinicopathological features and poor clinical outcome of breast cancer patients.

DNA methylation is a biochemical process that modifies gene expression without changing the underlying DNA sequence, and this represents the molecular basis for imprinting and epigenetics. Recent reports have revealed alterations in DNA methylation profiles in the placenta of babies born from assisted reproductive technologies (ART). This supports several previous observations that suggested an increase in the prevalence of imprinting diseases following ART treatment, and also fits our observations regarding the metabolism and requirements of early human embryos. Human embryo culture media (HECM) are currently formulated according to requirements based on the mouse embryo model, and in fact need to pass the Mouse Embryo Assay test in order to be accepted by the relevant authorities, despite the fact that physiological (especially the time necessary to reach genomic activation) and biochemical requirements of mouse and human embryos are quite different. This commentary aims to explain some of the discrepancies, and emphasize why human embryo metabolism tells us that the composition of HECM, as well as the role of the MEA as a unique model, should be re-evaluated. [ABSTRACT FROM AUTHOR]

Abstract: Dried blood spot samples (DBSS) on filter paper offer several advantages compared to conventional serum/plasma samples: they do not require any phlebotomy or separation of blood by centrifugation; they are less invasive; they allow sample stability and shipment at room temperature; and they pose a negligible risk of infection with blood-borne viruses, such as HIV, HBV and HCV, to those who handle them. Therefore dried blood spot samples (DBSS) on filter paper can be a quick, convenient and inexpensive means of obtaining blood samples for biomarker discovery, disease screening, diagnosis and treatment monitoring in non-hospitalized, public health settings. In this study, we investigated for the first time the potential application of dried blood spot samples (DBSS) in protein expression profiling using antibody array technology. First, optimal conditions for array assay performance using dried blood spot samples (DBSS) was established, including sample elution buffer, elution time, elution temperature and assay blocking buffer. Second, we analyzed dried blood spot samples (DBSS) using three distinct antibody array platforms, including sandwich-based antibody arrays, quantitative antibody arrays and biotin-label-based antibody arrays. In comparison with paired serum samples, detection of circulating proteins in dried blood spot samples (DBSS) correlated well for both low- and high-abundance proteins on all three antibody array platforms. In conclusion, our study strongly indicates the novel application of multiplex antibody array platforms to analyze dried blood spot samples (DBSS) on filter paper represents a viable, cost-effective method for protein profiling, biomarker discovery and disease screening in a large, population-based survey. [Copyright &y& Elsevier]

Although effluent treatment systems within pulp and paper mills remove many toxicants and improve wastewater quality, there is a need to understand and quantify the effectiveness of the treatment process. At a combined news and kraft pulp and paper mill in northwestern Ontario, Canada, fathead minnow (FHM) reproduction and physiology were examined before, during, and after a short-term (6-d) exposure to 10% (v/v) untreated kraft mill effluent (UTK), 25% (v/v) secondary treated kraft mill effluent (TK), and 100% (v/v) combined mill outfall (CMO). Although UTK exposure significantly decreased egg production, neither TK nor CMO caused any reproductive changes. The expression of six genes responsive to endocrine-disrupting compounds, stress, or metals was then examined in livers of these fish using real-time polymerase chain reaction. In female FHMs, none of the three effluents induced significant expression changes in any genes investigated. By contrast, in males there were significant increases in the mRNA levels of androgen receptor, estrogen receptor (ER) β, and cytochrome P4501A (CYP1A) upon UTK and TK exposure but no changes in ERα or vitellogenin (VTG) gene expression, whereas CMO exposure significantly increased the mRNA levels of ERα, VTG, and CYP1A. Together, these results suggest that kraft effluent before and after biological treatment contained compounds able to induce androgenic effects in FHMs, and that combination of kraft and newsmill effluents eliminated the androgenic compounds while inducing distinct and significant patterns of gene expression changes that were likely due to estrogenic compounds produced by the newsmill. Environ. Toxicol. Chem. 2010;29:430–439. © 2009 SETAC [ABSTRACT FROM AUTHOR]

Tremendous progress has been made in the design and implementation of synthetic gene circuits, but real-world applications of such circuits have been limited. Cell-free circuits embedded on paper developed by Pardee et al. promise to deliver specific and rapid diagnostics on a low-cost, highly scalable platform. [ABSTRACT FROM AUTHOR]

Aging is associated with substantial physiological changes and constitutes a major risk factor for neurological disorders including dementia. Alterations in gene expression upon aging have been extensively studied; however, an in-depth characterization of post-transcriptional regulatory events remains elusive. Here, we profiled the age-related changes of the transcriptome and translatome in the female mouse hippocampus by RNA sequencing of total RNA and polysome preparations at four ages (3-, 6-, 12-, 20-month-old); and we implemented a variety of bioinformatics approaches to unravel alterations in transcript abundance, alternative splicing, and polyadenylation site selection. We observed mostly wellcoordinated transcriptome and translatome expression signatures across age including upregulation of transcripts related to immune system processes and neuroinflammation, though transcripts encoding ribonucleoproteins or associated with mitochondrial functions, calcium signaling and the cell-cycle displayed substantial discordant profiles, suggesting translational control associated with age-related deficits in hippocampal-dependent behavior. By contrast, alternative splicing was less preserved, increased with age and was associated with distinct functionally-related transcripts encoding proteins acting at synapses/dendrites, RNA-binding proteins; thereby predicting regulatory roles for RBM3 and CIRBP. Only minor changes in polyadenylation site selection were identified, indicating pivotal 3'-end selection in young adults compared to older groups. Overall, our study provides a comprehensive resource of age-associated post-transcriptional regulatory events in the mouse hippocampus, enabling further examination of the molecular features underlying age-associated neurological diseases. [ABSTRACT FROM AUTHOR]

Abstract: The toxicity of pulp and paper mill effluents (PPMEs) has been greatly decreased, yet some continue to negatively affect fish reproduction. We hypothesized that PPMEs are affecting the brain resulting in decreased reproductive performance. Our goal was to use gene expression profiling to test the hypothesis that PPMEs are having an effect on neural systems in the fathead minnow (FHM; Pimephales promelas) in vivo. Sexually mature male and female FHM were exposed to 100% final biotreated PPMEs from 5 different sources for 5 days. Using an oligo-array (15K genes) we examined the effect of PPMEs on gene expression in the hypothalamus of female fish. We validated selected genes (cholecystokinin, RevErbβ2, and urotensin I) that were identified by microarray analysis using real-time reverse-transcriptase polymerase chain reaction (RT-PCR). We compared the FHM microarray dataset to multiple microarray datasets from experiments conducted with goldfish injected with different dopaminergic pharmaceuticals to examine whether PPMEs could be affecting the dopamine system. Exposure of FHM to PPMEs resulted in varying degrees of spawning inhibition. Microarray analysis revealed surprisingly few genes in the brain that were commonly affected by the different PPMEs. Real-time RT-PCR confirmed the changes in expression for cholecystokinin, RevErbβ2, and urotensin I. Comparison of the FHM and goldfish microarray datasets suggest that some PPMEs may be acting on the dopamine system. We show that PPMEs are neuroactive in fish and may be acting through some of the pathways in a manner similar to dopamine. [ABSTRACT FROM AUTHOR]

Endocrine disrupting compounds (EDCs) are chemicals that negatively impact endocrine system function, with effluent from paper mills one example of this class of chemicals. In Florida, female Eastern mosquitofish (Gambusia holbrooki) have been observed with male secondary sexual characteristics at three paper mill-impacted sites, indicative of EDC exposure, and are still found at one site on the Fenholloway River. The potential impacts that paper mill effluent exposure has on the G. holbrooki endocrine system and the stream ecosystem are unknown. The objective of this study was to use gene expression analysis to determine if exposure to an androgen receptor agonist was occurring and to couple this analysis with in vitro assays to evaluate the presence of androgen and progesterone receptor active chemicals in the Fenholloway River. Focused gene expression analyses of masculinized G. holbrooki from downstream of the Fenholloway River paper mill were indicative of androgen exposure, while genes related to reproduction indicated potential progesterone exposure. Hepatic microarray analysis revealed an increase in the expression of metabolic genes in Fenholloway River fish, with similarities in genes and biological processes compared to G. holbrooki exposed to androgens. Water samples collected downstream of the paper mill and at a reference site indicated that progesterone and androgen receptor active chemicals were present at both sites, which corroborates previous chemical analyses. Results indicate that G. holbrooki downstream of the Fenholloway River paper mill are impacted by a mixture of both androgens and progesterones. This research provides data on the mechanisms of how paper mill effluents in Florida are acting as endocrine disruptors. [ABSTRACT FROM AUTHOR]

Major depressive disorder (MDD) is a heritable disease with a heavy personal and socio-economic burden. Antidepressants of different classes are prescribed to treat MDD, but reliable and reproducible markers of efficacy are not available for clinical use. Further complicating treatment, the diagnosis of MDD is not guided by objective criteria, resulting in the risk of under- or overtreatment. A number of markers of MDD and antidepressant response have been investigated at the genetic, epigenetic, gene expression and protein levels. Polymorphisms in genes involved in antidepressant metabolism (cytochrome P450 isoenzymes), antidepressant transport (ABCB1), glucocorticoid signalling (FKBP5) and serotonin neurotransmission (SLC6A4andHTR2A) were among those included in the first pharmacogenetic assays that have been tested for clinical applicability. The results of these investigations were encouraging when examining patient-outcome improvement. Furthermore, a nine-serum biomarker panel (includingBDNF, cortisol and soluble TNF-α receptor type II) showed good sensitivity and specificity in differentiating between MDD and healthy controls. These first diagnostic and response-predictive tests for MDD provided a source of optimism for future clinical applications. However, such findings should be considered very carefully because their benefit/cost ratio and clinical indications were not clearly demonstrated. Future tests may include combinations of different types of biomarkers and be specific for MDD subtypes or pathological dimensions. [ABSTRACT FROM PUBLISHER]

Abstract: This study investigates the predictive ability of gene-expression programming (GEP) in the estimation of methane yield (Y m ) and effluent substrate (S e ) produced by two anaerobic filters. The modeling study was carried out using the data obtained from two upflow anaerobic filters – one mesophilic (35°C) and one thermophilic (55°C) – operated for the treatment of paper-mill wastewater under varying organic loadings. The GEP model was composed of three inputs, hydraulic retention time (T hr ), organic loading rate (R ol ), and influent substrate (S i ), and one output, either S e or Y m . The Stover–Kincannon model was also used for data analysis and to evaluate the prediction ability. Three statistical criteria, root mean square error (RMSE), determination coefficient (R 2), and Akaike''s information criteria (AIC), were the means used for comparison. The results showed that the GEP approach predicted the performance of both anaerobic filters much better than the Stover–Kincannon model. [Copyright &y& Elsevier]

Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Analyses of the molecular foundations of phenotypic plasticity are challenging, however, especially in the case of complex social phenotypes. Here we apply a machine learning approach to tackle this challenge by analyzing individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen. We find that caste-associated gene expression profiles respond strongly to queen loss, and that this change is partly explained by attributes such as age but occurs even in individuals that appear phenotypically unaffected. These results demonstrate that large changes in gene expression may occur in the absence of outwardly detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic level but not at the levels of ovarian development or behavior. Connecting genotypes to complex social behaviour is challenging. Taylor et al. use machine learning to show a strong response of caste-associated gene expression to queen loss, wherein individual wasp's expression profiles become intermediate between queen and worker states, even in the absence of behavioural changes. [ABSTRACT FROM AUTHOR]

Pathotyping and subtyping of influenza A virus were performed with a packaged paper fluidic-based analytical microdevice (PFAM) after one-step reverse transcription-polymerase chain reaction (RT-PCR). The PFAM contains two test lines: one for detecting M gene to identify the influenza A virus and another for haemagglutinin subtyping to determine the viral strain among H1N1, H3N2, and H5N1. The M gene and the haemagglutinin gene (H1, H3, and H5 genes) were amplified by using the Digoxigenin and the Texas Red modified primers, respectively, in the multiplex RT-PCR. The amplicon products were loaded in the conjugate pad of the PFAM in which the streptavidin coated gold nanoparticles were linked with the biotin moieties that were incorporated in the middle of the DNA strands, and then captured by the anti-Digoxigenin and anti-Texas Red immobilized on the test lines. Influenza A H1N1, H3N2, and H5N1 could be identified with a limit of detection of 102 copies of RNA templates in 10min. Pathotyping and subtyping of the clinical nasopharyngeal swab samples were also analyzed whose results were confirmed by real-time RT-PCR. [ABSTRACT FROM AUTHOR]

Abstract: The presence of unidentified estrogens and androgens in effluents from pulp and paper mills is well documented. However, their role in effluent effects on fish reproduction remains unclear. The objective of this study was to investigate the hypothesis that reproductive impacts of a modern pulp mill effluent are mediated by androgens and/or estrogens in the effluent. Male and female threespine stickleback were exposed to biologically treated Canadian bleached kraft mill effluent under flow-through conditions in the laboratory at 0, 1, 10 and 100% (v/v) dilutions. After 7 and 21 d of exposure, steroidogenesis was assessed using in vitro incubations of gonadal tissue in both males and females. mRNA expression of the estrogen-regulated gene vitellogenin, and the androgen-responsive gene spiggin were assessed using quantitative RT-PCR in the livers of male and posterior kidneys of female stickleback, respectively. Hepatic 7-ethoxyresorufin-O-deethylase (EROD) activity was assessed in both sexes. Effluent extracts were examined for estrogenic and androgenic bioactivity using receptor binding bioassays, and were screened for pulp and paper related extractives and steroidal androgens using GC–MS. This effluent up-regulated spiggin mRNA in the kidney of female stickleback at 10% and 100% (v/v) effluent at 21 d, but not at 7 d of exposure. This change at the mRNA expression of the gene was associated with an increase in cell height in kidney proximal tubule epithelial cells at 100% effluent after both 7 and 21 d. Liver vitellogenin mRNA in male stickleback was not induced at either 7 or 21 d. EROD was induced at 10 and 100% after 21 d of exposure in both sexes, but not after 7 d of exposure. Despite evidence of exposure to androgens, there was no reduction in steroidogenic capacity at any effluent dilution. Effluent extracts were capable of eliciting the displacement of androgens and estrogens from receptors, but androgenic potency was 4-fold greater. A screen of more than 30 androgenic androstane steroids showed no detections. Hence, the androgenic constituents in this particular effluent remain unknown. [Copyright &y& Elsevier]

Background: Spinal cord injury (SCI) is a nervous system disease leading to motor and sensory dysfunction below the injury level, and can result in paralysis. MicroRNAs (miRNAs) play a key role in SCI treatment, and related research provides insights for SCI diagnosis and treatment. Bibliometrics is an important tool for literature statistics and evaluation, objectively summarizing multidimensional information. This study comprehensively overviews the field through bibliometric analysis of miRNA and SCI research, providing contemporary resources for future collaboration and clinical treatment. Materials and methods: In this study, we searched the Web of Science Core Collection (WOSCC) database. After careful screening and data import, we extracted annual publications, citation counts, countries, institutions, authors, journals, highly cited articles, co-cited articles, keywords, and H-index. Bibliometrics and visualization analyses employed VOSviewer, CiteSpace, the R package "bibliometrix," and online analytic platforms. Using Arrowsmith, 1 we determined miRNA-SCI relationships and discussed potential miRNA mechanisms in SCI. Results: From 2008 to 2024, the number of related papers increased annually, reaching 754. The number of yearly publications remained high and entered a period of rapid development. Researchers from 50 countries/regions, 802 institutions, 278 journals, and 3,867 authors participated in the field. Currently, China has advantages in the number of national papers, citations, institutions, and authors. However, it is necessary to strengthen cooperation among different authors, institutions, and countries to promote the production of important academic achievements. The research in the field currently focuses on nerve injury, apoptosis, and gene expression. Future research directions mainly involve molecular mechanisms, clinical trials, exosomes, and inflammatory reactions. Conclusion: Overall, this study comprehensively analyzes the research status and frontier of miRNAs in SCI. A systematic summary provides a complete and intuitive understanding of the relationship between SCI and miRNAs. The presented findings establish a basis for future research and clinical application in this field. [ABSTRACT FROM AUTHOR]

Abstract: A xylanase gene (xynG1-1) from Paenibacillus campinasensis G1-1 was expressed in Bacillus megaterium MS941 and a high level of extracellular xylansae activity (304.26IU/mL) was achieved after induction with 0.5% xylose. The purified recombinant xylanase (XynG1-1R) revealed optimal activity at 60°C and pH 7.0 and retained 79% and 81% activity after incubation without substrate at 60°C, pH 5.0 and pH 8.0 for 3h, respectively. Application of XynG1-1R (15IU/g pulp) to cotton stalk pulp bleaching increased brightness by 3.65% over that of the control without the xylanase and reduced the need for chlorine compounds by 50% without loss of brightness and pulp fiber qualities. When XynG1-1R (80IU/g paper sludge) was used in combination with mixed cellulolytic enzymes, the saccharification efficiency of recycled paper sludge was increased by 10%. These results indicated that XynG1-1R is a promising candidate for various industrial applications such as biobleaching and bioenergy conversion. [Copyright &y& Elsevier]

Abstract: The “Operon paper” by F. Jacob and J. Monod started 50 years of research into understanding how the expression of genes is regulated on a molecular level. Ten years ago, microRNAs (miRNAs) emerged as major regulators of eukaryotic gene expression. Here, I will review the basic principles of gene regulation by miRNAs and how these principles can be linked to insights from the Operon paper. A lot of what is understood about miRNAs required a combination of computational and experimental methods. I will discuss some examples that illustrate the power of this approach. [Copyright &y& Elsevier]

Herein, we report the development of a novel, inexpensive, and portable filter-paper-based strip biosensor for the detection of bacterial quorum sensing signaling molecules, N-acylhomoserine lactones (AHLs). AHLs are generally employed by Gram-negative bacteria for their cell-cell communication to control expression of specialized genes, such as those involved in biofilm formation and production of virulence factors, in a populationdensity-dependent manner. First, a bacterial cell-based sensing system employing components of ABE-mediated QS regulatory system as recognition elements and β-galactosidase as the reporter protein was designed and developed. The bacterial-sensing cells were then liquiddried on strips of filter paper. β-Galactosidase as the reporter allows for the visual monitoring of the analyteinduced signal when a colorimetric method of detection is applied. The paper strip biosensor was able to detect low ABE concentrations down to 1 x 10 M. Furthermore, it was successfully applied to the detection of AHLs in physiological samples, such as saliva. The filter-paper-based sensing strips could provide reproducible results upon storage at 4 °C for at least 3 months. In conclusion, a filter-paper-based strip biosensor was developed that allows for visual, fast, and convenient detection of ARts in a dose-dependent manner in a test sample. In addition, it does not require expensive equipment or trained personnel and allows ease of transportation and storage. Therefore, we envision that this biosensor will serve as a simple and economical portable field kit for on-site monitoring of AHL in a variety of clinical and environmental samples. [ABSTRACT FROM AUTHOR]

Abstract: We evaluated plasma testosterone (T) and 17β-estradiol (E2) levels and ovarian aromatase CYP19a gene expression following a single intraperitoneal injection of Chilean pulp and paper mill effluent extracts into juvenile triploid rainbow trout. Fish injected with untreated effluent extracts had increased plasma T after 4 days, while plasma E2 concentration was increased in fish injected with both primary and secondary treated effluent extracts at the same sampling period. Ovarian CYP19a gene expression as measured by qRT-PCR was significantly induced in fish injected with the untreated, primary and secondary treated pulp and paper mill effluent extracts. Similar induction of CYP19a expression was found in fish injected with the androgens androstenedione (ADD) and T. A Principal Component Analysis (PCA) was conducted in order to identify structure in relationships between all measured variables and identifying which factors were most responsible for the variance observed within the plasma steroid levels, upregulation of ovarian CYP19a gene expression and the final estrogenic effect of increased plasma VTG levels. This analysis indicated a cluster correlation between plasma T levels and CYP19a gene expression (Factor 1, explaining 27.2% of total variance), a cluster including condition factor and liver somatic index (Factor 2, explaining 17.3%) and an additional cluster including plasma E2 and vitellogenin levels (Factor 3, explaining an additional 15.8%). The present results indicate that Chilean pulp and paper mill effluent extracts cause estrogenic effects in triploid rainbow trout. These effects could be related to the compounds present in the effluent that act as estrogen receptor agonists, or that induce changes leading to increased amounts of endogenous estrogens, reflected by increased E2 levels and induced aromatase expression/activity. [Copyright &y& Elsevier]

Effluents from pulp and paper mills that historically have used elemental chlorine in the bleaching process have been implicated in inhibiting reproduction in fish. Compounds with estrogenic and androgenic binding affinities have been found in these effluents, suggesting that the impairment of reproduction is through an endocrine-related mode of action. To date, a great deal of attention has been paid to phytoestrogens and resin acids that are present in mill process streams as a result of pulping trees. Estrogen and estrogen mimics interact directly with the estrogen receptor and have near immediate effects on gene transcription by turning on the expression of a unique set of genes. Using differential display (DD) RT-PCR, we examined changes in gene expression induced by exposure to paper mill effluents. Largemouth bass were exposed to 0, 10, 20, 40, and 80% paper mill effluent concentrations in large flow-through tanks for varied periods of time including 7, 28 or 56 days. Plasma hormone levels in males and females and plasma vitellogenin (Vtg) in females decreased with dose and time. Measurements of changes in gene expression using DD RT-PCR suggest that the gene expression patterns of male fish do not change much with exposure, except for the induction of a few genes including CYP 1A, a protein that is induced through the action of the Ah receptor in response to dioxin and similar polyaromatic hydrocarbons. However, in the case of females, exposure to these effluents resulted in an up-regulation of CYP 1A that was accompanied by a generalized down-regulation of genes normally expressed during the reproductive season. These antiestrogenic changes are in agreement with previous studies in bass exposed to these effluents, and could result in decreased reproductive success in affected populations. [Copyright &y& Elsevier]

Background: Schizophrenia is a complex neuropsychiatric disorder of unclear etiology. The strongest known genetic risk factor is the 22q11.2 microdeletion. Research has yet to confirm which genes within the deletion region are implicated in schizophrenia. The minimal 1.5 megabase deletion contains MIR185, which encodes microRNA 185. Methods: We determined miR-185 expression in embryonic and adult mouse brains. Common and rare variants at this locus were then investigated using a human genetics approach. First, we performed gene-based analyses for MIR185 common variants and target genes using Psychiatric Genomics Consortium genome-wide association data. Second, MIR185 was resequenced in German patients (n = 1000) and controls (n = 500). We followed up promising variants by genotyping an additional European sample (patients, n = 3598; controls, n = 4082). Results: In situ hybridization in mice revealed miR-185 expression in brain regions implicated in schizophrenia. Gene-based tests revealed association between common variants in 3 MIR185 target genes (ATAT1, SH3PXD2A, NTRK3) and schizophrenia. Further analyses in mice revealed overlapping expression patterns for these target genes and miR185. Resequencing identified 2 rare patient-specific novel variants flanking MIR185. However, follow-up genotyping provided no further evidence of their involvement in schizophrenia. Limitations: Power to detect rare variant associations was limited. Conclusion: Human genetic analyses generated no evidence of the involvement of MIR185 in schizophrenia. However, the expression patterns of miR-185 and its target genes in mice, and the genetic association results for the 3 target genes, suggest that further research into the involvement of miR-185 and its downstream pathways in schizophrenia is warranted. [ABSTRACT FROM AUTHOR]

BACKGROUND: In a genome-wide association study of autism, zinc finger protein 804A (ZNF804A) single nucleotide polymorphisms (SNPs) were found to be nominally associated in verbally deficient individuals with autism. Zinc finger protein 804A copy number variations (CNVs) have also been observed in individuals with autism. In addition, ZNF804A is known to be involved in theory of mind (ToM) tasks, and ToM deficits are deemed responsible for the communication and social challenges faced by individuals with autism. We hypothesized that ZNF804A could be a risk gene for autism. METHODS: We examined the genetic association and CNVs of ZNF804A in 841 families in which 1 or more members had autism. We compared the expression of ZNF804A in the postmortem brains of individuals with autism (n = 8) and controls (n = 13). We also assessed in vitro the effect of ZNF804A silencing on the expression of several genes known to be involved in verbal efficiency and social cognition. RESULTS: We found that rs7603001 was nominally associated with autism (p = 0.018). The association was stronger (p = 0.008) in the families of individuals with autism who were verbally deficient (n = 761 families). We observed ZNF804A CNVs in 7 verbally deficient boys with autism. In ZNF804A knockdown cells, the expression of synaptosomal-associated protein, 25kDa (SNAP25) was reduced compared with controls (p = 0.009). The expression of ZNF804A (p = 0.009) and SNAP25 (p = 0.009) were reduced in the anterior cingulate gyrus (ACG) of individuals with autism. There was a strong positive correlation between the expression of ZNF804A and SNAP25 in the ACG (p < 0.001). LIMITATIONS: Study limitations include our small sample size of postmortem brains. CONCLUSION: Our results suggest that ZNF804A could be a potential candidate gene mediating the intermediate phenotypes associated with verbal traits in individuals with autism. [ABSTRACT FROM AUTHOR]

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Abstract: To improve the β-glucosidase yield and total cellulase activity of Trichoderma reesei, extracellular β-glucosidase (BGLI) was overexpressed under the control of the modified four-copy cbh1 promoter. Three transformants B2, B12 and B15 with successful integration of the bgl1 gene expression cassette were obtained, which exhibited 3.7-, 2.0- and 1.8-fold increase in β-glucosidase activity than the parental strain RUT C30, respectively. The filter paper activities of the productive transformants B12 and B15 were improved by up to 130% and 55%, respectively. Saccharification of corncob residue with the crude enzyme dosages showed that the reducing sugar yields of B12 (5.59mg/ml) and B15 (4.80mg/ml) were 29% and 11% higher than that of RUT C30 (4.34mg/ml), respectively. The present results proved that the modified four-copy cbh1 promoter was a useful tool for improving the cellulase activity of T. reesei, and the engineering strains developed in this study could be potentially used as promising cell factories for β-glucosidase or cellulase production. [ABSTRACT FROM AUTHOR]

This document is a summary of a special issue of the International Journal of Molecular Sciences titled "The Molecular and Cellular Pathophysiologic Mechanisms Underlying Ocular Diseases and Emerging Therapies." The special issue focuses on the prevalence and rising global public health concerns of visual impairment and ophthalmic diseases. It aims to enhance researchers' and eyecare professionals' understanding of the risk factors, biomarkers, and cellular and molecular mechanisms underlying various eye diseases. The special issue includes eight papers, including original research papers, reviews, and a case report, covering topics such as diabetic retinopathy, retinal diseases, tear biomarkers, and uveal melanoma. The papers provide new advancements in the molecular and cellular pathogenesis of eye diseases and the development of preventive measures and emerging therapies. The document concludes by expressing hope that the special issue will inspire further research and understanding of eye diseases. [Extracted from the article]