DEAD-box helicase 1 inhibited CD8+ T cell antitumor activity by inducing PD-L1 expression in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) does not respond well to current treatments, even immune checkpoint inhibitors. PD-L1 (programmed cell death ligand 1 or CD274 molecule)-mediated immune escape of tumor cells may be a key factor affecting the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the regulatory mechanisms of PD-L1 expression and immune escape require further exploration. Here, we observed that DDX1 (DEAD-box helicase 1) was overexpressed in HCC tissues and associated with poor prognosis in patients with HCC. Additionally, DDX1 expression correlated negatively with CD8+ T cell frequency. DDX1 overexpression significantly increased interferon gamma (IFN-γ)-mediated PD-L1 expression in HCC cell lines. DDX1 overexpression decreased IFN-γ and granzyme B production in CD8+ T cells and inhibited CD8+ T cell cytotoxic function in vitro and in vivo. In conclusion, DDX1 plays an essential role in developing the immune escape microenvironment, rendering it a potential predictor of ICI therapy efficacy in HCC.

A novel signature incorporating lipid metabolism- and immune-related genes to predict the prognosis and immune landscape in hepatocellular carcinoma.

Background: Liver hepatocellular carcinoma (LIHC) is a highly malignant tumor with high metastasis and recurrence rates. Due to the relation between lipid metabolism and the tumor immune microenvironment is constantly being elucidated, this work is carried out to produce a new prognostic gene signature that incorporates immune profiles and lipid metabolism of LIHC patients. Methods: We used the "DEseq2" R package and the "Venn" R package to identify differentially expressed genes related to lipid metabolism (LRDGs) in LIHC. Additionally, we performed unsupervised clustering of LIHC patients based on LRDGs to identify their subgroups and immuno-infiltration and Gene Ontology (GO) enrichment analysis on the subgroups. Next, we employed multivariate, LASSO and univariate Cox regression analyses to determine variables and to create a prognostic profile on the basis of immune- and lipid metabolism-related differential genes (IRDGs and LRDGs). We separated patients into low- and high-risk groups in accordance with the best cut-off value of risk score. We conducted Decision Curve Analysis (DCA), Receiver Operating Characteristic curve analysis as a function of time as well as Survival Analysis to evaluate this signature's prognostic value. We incorporated the clinical characteristics of patients into the risk model to obtain a nomogram prognostic model. GEO14520 and ICGC-LIRI JP datasets were employed to externally confirm the accuracy and robustness of signature. The gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were applied for investigating the underlying mechanisms. Immune infiltration analysis was implemented to examine the differences in immune between both risk groups. Single-cell RNA sequencing (scRNA-SEQ) was utilized to characterize the genes that were involved in the distribution of signature and expression characteristics of different LIHC cell types. The patients' sensitivity in both risk groups to commonly used chemotherapeutic agents and semi-inhibitory concentrations (IC50) of the drugs was assessed using the GDSC database. On the basis of the differentially expressed genes (DEGs) in the two groups, the CMAP database was adopted for the prediction of potential small-molecule compounds. Small-molecule compounds were molecularly docked with prognostic markers. Lastly, we investigated the prognostic gene expression levels in normal and LIHC tissues with immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction(qRT-PCR). Results: We built and verified a prognostic signature with seven genes that incorporated immune profiles and lipid metabolism. Patients were classified as low- and high-risk groups depending on their prognostic profiles. The overall survival (OS) was markedly lower in the high-risk group as compared to low-risk group. Time-dependent ROC curves more precisely predicted patients' survival at 1, 3 and 5 years; the area under the ROC curve was 0.81 (1 year), 0.75 (3 years) and 0.77 (5 years). The DCA curves showed the value of the prognostic genes in this signature for clinical applications. We included the patients' clinical characteristics in the risk model for both multivariate and univariate Cox regression analyses, and the findings revealed that the risk model represents an independent factor that influences OS in LIHC patients. With immune analysis, GSVA and GSEA, we identified that there are remarkable differences between the two risk groups in immune pathways, lipid metabolism, tumor development, immune cell infiltration and immune microenvironment, response to immunotherapy, and sensitivity to chemotherapy. Moreover, those with higher risk scores presented greater sensitivity to the chemotherapeutic agents. Experiments in vitro further elucidated the roles of SPP1 and FLT3 in the LIHC immune microenvironment. Furthermore, four small-molecule drugs that could target LIHC were screened. In vitro qRT-PCR , IHC revealed that the SPP1,KIF18A expressions were raised in LIHC in tumor samples, whereas FLT3,SOCS2 showed the opposite trend. Conclusions: We developed and verified a new signature comprising immune- and lipid metabolism-associated markers and to assess the prognosis and the immune status of LIHC patients. This signature can be applied to survival prediction, individualized chemotherapy, and immunotherapeutic guidance for patients with liver cancer. This study also provides potential targeted therapeutics and novel ideas for the immune evasion and progression of LIHC.

Integrative analysis of disulfidptosis and immune microenvironment in hepatocellular carcinoma: a putative model and immunotherapeutic strategies.

Background: Hepatocellular carcinoma (HCC) is a malignant tumor with a high rate of recurrence and m metastasis that does not respond well to current therapies and has a very poor prognosis. Disulfidptosis is a novel mode of cell death that has been analyzed as a novel therapeutic target for HCC cells. Methods: This study integrated bulk ribonucleic acid (RNA) sequencing datasets, spatial transcriptomics (ST), and single-cell RNA sequencing to explore the landscape of disulfidptosis and the immune microenvironment of HCC cells. Results: We developed a novel model to predict the prognosis of patients with HCC based on disulfidptosis. The model has good stability, applicability, and prognostic and immune response prediction abilities. N-myc downregulated gene1 (NDRG1) may contribute to poor prognosis by affecting macrophage differentiation, thus allowing HCC cells to evade the immune system. Conclusion: Our study explores the disulfidptosis of HCC cells through multi-omics and establishes a new putative model that explores possible targets for HCC treatment.

RNA m6A methyltransferase METTL3 promotes colorectal cancer cell proliferation and invasion by regulating Snail expression.

Nitrogen 6-methyladenosine (m6A) is the result of methylation of nitrogen-6 on adenosine, and is the most abundant chemical modification of eukaryotic mRNA. Dysregulation of m6A methylation has been implicated in cancer development and progression through various mechanisms. This type of methylation is primarily regulated by methyltransferase-like 3 (METTL3). However, the molecular mechanisms underlying the role of METTL3 in colorectal cancer (CRC) have not been extensively elucidated. The present study explored m6A modification and the underlying mechanism of m6A, which serve regulatory roles in the development of CRC. It was found that METTL3 is upregulated in CRC cell lines and tissues, and its expression positively correlated with poor overall survival (OS). Mechanistically, the present study demonstrated that METTL3 methylates Snail mRNA, thus stabilizing it to promote CRC malignancy. The present findings indicate that m6A modification is involved in CRC tumorigenesis, and highlight its potential as a therapeutic target against CRC.

Amplification of RAD54B promotes progression of hepatocellular carcinoma via activating the Wnt/ß-catenin signaling.

Liver cancer was reported to be the sixth most frequently diagnosed cancer, and hepatocellular carcinoma (HCC) accounts for 75%-85% of primary liver cancer. Nevertheless, the concrete molecular mechanisms of HCC progression remain obscure, which is essential to elucidate. The expression profile of RAD54B in HCC was measured using qPCR and western blotting. Moreover, the levels of RAD54B in paraffin-embedded samples were evaluated using immunohistochemistry (IHC). The effect of RAD54B on HCC progression was testified by in vitro experiments, and in vivo orthotopic xenograft tumor experiments. The mechanisms of RAD54B promoting HCC progression were investigated through molecular and function experiments. Herein, RAD54B are dramatically upregulated in HCC tissues and cell lines both on mRNA and protein levels, and RAD54B can servers as an independent prognostic parameter of 5-year overall survival and 5-year disease-free survival for patients with HCC. Moreover, up-regulation of RAD54B dramatically increases the capacity for in vitro cell viability and motility, and in vivo intrahepatic metastasis of HCC cells. Mechanistically, RAD54B promotes the HCC progression through modulating the wnt/ß-catenin signaling. Notably, blocking the wnt/ß-catenin signaling axis can counteract the activating effects of RAD54B on motility of HCC cells. Besides, further analysis illustrates that DNA amplification is one of the mechanisms leading to mRNA overexpression of RAD54B in HCC. Our findings indicate that RAD54B might be a promising potential prognostic marker and a candidate therapeutic target to therapy HCC.

A rapid and inexpensive method for the isolation and identification of Giardia.

This work details a protocol for the isolation of Giardia species from their host animals and their identification based on their morphological and molecular characteristics. Giardia are intestinal protozoan parasites found in almost all vertebrates and the epidemiology of Giardia has attracted the attention of scientists due to their harm to humans and live stocks worldwide. Giardia trophozoites adhere to the surface of host's intestines using their ventral disc, and they also adhere the culture tube wall during in vitro culturing. We developed a method of isolating Giardia trophozoites according to this phenomenon, and a method of isolating Giardia cysts according to their special density as well. We validated the protocol by isolating and identifying Giardia species from their host animals, and all the results support that this methodology has a certain validity. It could help the further epidemiological researches and other researches requiring relatively pure living organism as materials of this harmful parasite.•An isolation method with high efficiency which remains the physiological activity of isolated Giardia.•An identification method with high accuracy which avoids the influences from other organisms.•Low-cost, fast and convenient methodology.

The ubiquity and coexistence of two FBPases in chloroplasts of photosynthetic eukaryotes and its evolutionary and functional implications.

In photosynthetic eukaryotes, there are two well-characterized fructose-1,6-bisphosphatases (FBPases): the redox-insensitive cytosolic FBPase (cyFBPase), which participates in gluconeogenesis, and the redox-sensitive chloroplastic FBPase (cpFBPase1), which is a critical enzyme in the Calvin cycle. Recent studies have identified a new chloroplastic FBPase, cpFBPase2; however, its phylogenetic distribution, evolutionary origin, and physiological function remain unclear. In this study, we identified and characterized these three FBPase isoforms in diverse, representative photosynthetic lineages and analyzed their phylogeny. In contrast to previous hypotheses, we found that cpFBPase2 is ubiquitous in photosynthetic eukaryotes. Additionally, all cpFBPase2s from diverse lineages form a monophyly, suggesting cpFBPase2 is not a recently evolved enzyme restricted to land plants but rather evolved early in the evolution of photosynthetic organisms, and most likely, in the common ancestor of photosynthetic eukaryotes. cyFBPase was probably first duplicated to produce cpFBPase2, and then the latter duplicated to produce cpFBPase1. The ubiquitous coexistence of these two cpFBPases in chloroplasts is most likely the consequence of adaptation to different redox conditions of photosynthesis, especially those caused by recurrent changes in light conditions.

An investigation of the prevalence of Giardia agilis in anuran amphibians from fourteen areas in China.

Giardia agilis is a Giardia species which is morphological distinguishable for its very narrow and elongated trophozoite. Although there were a few studies about its morphology since its first report in 1882, none investigations about its prevalence have ever been reported to date. We investigated the prevalence of G. agilis in 25 anuran amphibian species from five provinces of China using both morphological and molecular methods. Of the 463 tested samples, 195 (42.1%) were positive. The 195 positive samples were from nine species, which are scatteredly distributed in four anuran amphibian families. The statistical prevalence among adults of different frog species showed no significant difference, and so did among tadpoles. Thus, G. agilis is probably able to infect all anuran amphibians without species-bias. More interestingly, the prevalence in the tadpoles is significantly higher than in their adults. The prevalence in Kaloula verrucosa tadpoles from the same area showed no significant differences between none-legged stage and two-legged stage, but the prevalence in these two developmental stages is significantly higher than in the four-legged stage. And the prevalence in four-legged stage is still much higher than in adults. A turning point of prevalence appeared in the period of tadpole tail degeneration. Moreover, all the positive samples were from the areas with relatively high altitude (more than 870 m). The fact that G. agilis tends to easily infect the frogs living in high altitude areas indicated it has evolved the ability to adapted the dramatic temperature change in poikilothermal animals. Therefore, G. agilis has evolved some special successful parasitism strategies for parasitizing the poikilothermal hosts with metamorphosis such as anuran amphibians.

Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia.

BACKGROUND: The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes - protists were reported. Giardia lamblia, a protist with the controversy of whether it is an extreme primitive eukaryote or just a highly evolved parasite, might be an interesting object for carrying out the nucleolar proteome study of protists and for further examining the controversy. RESULTS: Using bioinformatics methods, we reconstructed G. lamblia nucleolar proteome (GiNuP) and the common nucleolar proteome of the three representative higher eukaryotes (human, Arabidopsis, yeast) (HEBNuP). Comparisons of the two proteomes revealed that: 1) GiNuP is much smaller than HEBNuP, but 78.4% of its proteins have orthologs in the latter; 2) More than 68% of the GiNuP proteins are involved in the "Ribosome related" function, and the others participate in the other functions, and these two groups of proteins are much larger and much smaller than those in HEBNuP, respectively; 3) Both GiNuP and HEBNuP have their own specific proteins, but HEBNuP has a much higher proportion of such proteins to participate in more categories of nucleolar functions. CONCLUSION: For the first time the nucleolar proteome of a protist - Giardia was reconstructed. The results of comparison of it with the common proteome of three representative higher eukaryotes -- HEBNuP indicated that the simplicity of GiNuP is most probably a reflection of primitiveness but not just parasitic reduction of Giardia, and simultaneously revealed some interesting evolutionary phenomena about the nucleolus and even the eukaryotic cell, compositionally and functionally.

Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment.

Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.

Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton.

BACKGROUND: Eukaryotic cells contain a huge variety of internally specialized subcellular compartments. Stoichiogenomics aims to reveal patterns of elements usage in biological macromolecules. However, the stoichiogenomic characteristics and how they adapt to various subcellular microenvironments are still unknown. RESULTS: Here we first updated the definition of stoichiogenomics. Then we applied it to subcellular research, and detected distinctive nitrogen content of nuclear and hydrogen, sulfur content of extracellular proteomes. Specially, we found that acidic amino acids (AAs) content of cytoskeletal proteins is the highest. The increased charged AAs are mainly caused by the eukaryotic originated cytoskeletal proteins. Functional subdivision of the cytoskeleton showed that activation, binding/association, and complexes are the three largest functional categories. Electrostatic interaction analysis showed an increased electrostatic interaction between both primary sequences and PPI interfaces of 3D structures, in the cytoskeleton. CONCLUSIONS: This study creates a blueprint of subcellular stoichiogenomic characteristics, and explains that charged AAs of the cytoskeleton increased greatly in evolution, which offer material basis for the eukaryotic cytoskeletal proteins to act in two ways of electrostatic interactions, and further perform their activation, binding/association and complex formation.

A new species of Giardia Künstler, 1882 (Sarcomastigophora: Hexamitidae) in hamsters.

BACKGROUND: Giardia spp. are flagellated protozoan parasites that infect humans and many other vertebrates worldwide. Currently seven species of Giardia are considered valid. RESULTS: Here, we report a new species, Giardia cricetidarum n. sp. in hamsters. Trophozoites of G. cricetidarum n. sp. are pear-shaped with four pairs of flagella and measure on average 14 µm (range 12-18 µm) in length and 10 µm (range 8-12 µm) in width. The trophozoites of the new species are generally larger and stouter than those of most of the other Giardia spp. and exhibit the lowest length/width ratio (c.1.40) of all recognized Giardia species. Cysts of G. cricetidarum n. sp. are ovoid and measure on average 11 µm (range 9-12 µm) in length and 10 µm (range 8-10 µm) in width and are indistinguishable from the cysts of other Giardia species. Molecular phylogenetic analyses based on beta-giardin, small subunit rRNA, and elongation factor-1 alpha loci all demonstrated that G. cricetidarum n. sp. is genetically distinct from all currently accepted Giardia spp. Investigation of the host range indicated that the new species was only found in hamsters (including Phodopus sungorus, P. campbelli and Mesocricetus auratus), while all the other described mammal-parasitizing species (G. muris, G. microti and G. intestinalis) each infect multiple hosts. Cross-transmission studies further demonstrated the apparent host specificity of G. cricetidarum n. sp. as it only infected hamsters. Trophozoites were found in high numbers in hamster intestines (5 × 105 - 5 × 106) and was rarely detected co-infecting with other Giardia spp. in the common hamster, suggesting it has some advantages in parasitizing hamsters. CONCLUSIONS: This study has identified a new species of Giardia, which appears to be specific to hamsters, and together with the three other mammal-parasitizing Giardia species with different host ranges, may be able to be used as a model system for the study of evolutionary divergence of host parasitism strategies in Giardia.

Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications.

BACKGROUND: It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Actually the reverse question -- how the few introns can be retained under the evolutionary selection pressure of intron loss -- is equally significant but was rarely studied, except that it was conjectured that the essential functions of some introns prevent their loss. The situation that extremely few (eight) spliceosome-mediated cis-spliced introns present in the relatively simple genome of Giardia lamblia provides an excellent opportunity to explore this question. RESULTS: Our investigation found three types of distribution patterns of the few introns in the intron-containing genes: ancient intron in ancient gene, later-evolved intron in ancient gene, and later-evolved intron in later-evolved gene, which can reflect to some extent the dynamic evolution of introns in Giardia. Without finding any special features or functional importance of these introns responsible for their retention, we noticed and experimentally verified that some intron-containing genes form sense-antisense gene pairs with transcribable genes on their complementary strands, and that the introns just reside in the overlapping regions. CONCLUSIONS: In Giardia's evolution, despite constant evolutionary selection pressure of intron loss, intron gain can still occur in both ancient and later-evolved genes, but only a few introns are retained; at least the evolutionary retention of some of the introns might not be due to the functional constraint of the introns themselves but the causes outside of introns, such as the constraints imposed by other genomic functional elements overlapping with the introns. These findings can not only provide some clues to find new genomic functional elements -- in the areas overlapping with introns, but suggest that "functional constraint" of introns may not be necessarily directly associated with intron loss and gain, and that the real functions are probably still outside of our current knowledge. REVIEWERS: This article was reviewed by Mikhail Gelfand, Michael Gray, and Igor Rogozin.

Giardia's primitive GPL biosynthesis pathways with parasitic adaptation 'patches': implications for Giardia's evolutionary history and for finding targets against Giardiasis.

Giardia is a worldwide spread protozoan parasite colonizing in small intestines of vertebrates, causing Giardiasis. The controversy about whether it is an extremely primitive eukaryote or just a highly evolved parasite has become a fetter to its uses as a model for both evolutionary and parasitological studies for years. Glycerophospholipid (GPL) synthesis is a conserved essential cellular process, and thus may retain some original features reflecting its evolutionary position, and this process should also have undergone parasitic adaptation to suit Giardia's dietary lipid-rich environment. Thus, GPL synthesis pathways may be a perfect object to examine the controversy over Giardia. Here, we first clarified Giardia's previously confusing GPL synthesis by re-identifying a reliable set of GPL synthesis genes/enzymes. Then using phylogenetic and comparative genomic analyses, we revealed that these pathways turn out to be evolutionarily primitive ones, but with many secondary parasitic adaptation 'patches' including gene loss, rapid evolution, product relocation, and horizontal gene transfer. Therefore, modern Giardia should be a mosaic of 'primary primitivity' and 'secondary parasitic adaptability', and to make a distinction between the two categories of features would restart the studies of eukaryotic evolution and parasitic adaptation using Giardia as a model system.

Overexpression of the long non-coding RNA, linc-UBC1, is associated with poor prognosis and facilitates cell proliferation, migration, and invasion in colorectal cancer.

Long non-coding RNAs (lncRNAs) serve comprehensive roles in various diseases, including cancer. lncRNA upregulated in bladder cancer 1 (linc-UBC1) is a notable biomarker of prognosis in certain cancer types; however, its involvement in the progression of colorectal cancer (CRC) remains unknown. The present study aimed to investigate the expression of linc-UBC1 in patients with CRC and to investigate its effect on CRC cells. The expression levels of linc-UBC1 were estimated by reverse transcription-quantitative polymerase chain reaction in clinical CRC specimens and matched adjacent non-tumor mucosa from 96 cases of CRC, as well as in a number of CRC cell lines. In addition, the biological roles of linc-UBC1 were examined using a cell counting kit-8 assay, flow cytometry, and migration and invasion assays following the downregulation of linc-UBC1 by small interfering RNA. The results revealed that linc-UBC1 was significantly overexpressed in CRC tissues and the majority of CRC cell lines compared with the matched non-tumor mucosa and normal intestinal epithelial cells. Furthermore, high expression levels of linc-UBC1 were significantly associated with large tumor size, greater tumor depth, lymph node metastasis, and advanced tumor-node-metastasis stages. Patients with abnormal expression of linc-UBC1 had poorer overall survival times according to Kaplan-Meier analyses. Furthermore, multivariate Cox regression analysis indicated that linc-UBC1 was a significant independent prognostic factor. The results also revealed that reducing the expression of linc-UBC1 led to the inhibition of migration, invasion, and proliferation of CRC cells in vitro. Taken together, the results of the present study suggest that overexpression of linc-UBC1 promotes proliferation and metastasis in CRC, and may be considered as a novel diagnostic marker of CRC.

DAT1 methylation is associated with methylphenidate response on oppositional and hyperactive-impulsive symptoms in children and adolescents with ADHD.

OBJECTIVES: To examine the association of the DNA methylation of DAT1 and DRD4 gene with methylphenidate (MPH) response in attention deficit hyperactivity disorder (ADHD). METHODS: One hundred and eleven DSM-IV defined ADHD Chinese Han children were recruited. Inattention, hyperactivity-impulsivity and oppositional symptoms were evaluated by the Swanson, Nolan and Pelham-IV-parent rating scale (SNAP-IV-P) at baseline and 6 weeks after MPH treatment. DNA methylation of CpG sites in the promoter sequences of DAT1 and DRD4 was examined for association with treatment response. RESULTS: Greater improvement on the SNAP-IV-P total score and percentage change from baseline score were both significantly correlated with DAT1 methylation (rho =-0.222, P = .019 and rho = -0.203, P = .032, respectively). A secondary analysis demonstrated that the effect of DAT1 methylation on symptom response was primarily related to the percentage change in oppositional symptoms (rho = -0.242; P = .012), with a smaller significant effect on hyperactivity-impulsivity (rho = -0.192; P = .045). No significant correlation was found between the treatment effect on inattention and DAT1 methylation (rho = -0.101; P = .292). No significant correlation was observed between mean DRD4 methylation and measures of treatment outcome or baseline symptoms. CONCLUSIONS: Our findings provide initial evidence for the involvement of the epigenetic alterations of DAT1 in modulating the response to MPH treatment in ADHD, primarily on oppositional and hyperactive-impulsive symptoms.

Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals.

Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.

Structural and evolutionary characteristics of pyruvate phosphate dikinase in Giardia lamblia and other amitochondriate protozoa.

BACKGROUND: Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the interconversion of phosphoenolpyruvate (PEP) and pyruvic acid, leading to catabolism and adenosine triphosphate (ATP) synthesis or gluconeogenesis and ATP consumption. Molecular modeling of PPDKs from divergent organisms demonstrates that the orientation of the phosphorylatable histidine residue within the central domain of PPDK determines whether this enzyme promotes catabolism or gluconeogenesis. The goal of this study was to determine whether PDDK from Giardia underwent adaptive evolution in order to produce more energy under anaerobic conditions. METHODS: A total of 123 PPDK sequences from protozoans, proteobacteria, plants, and algae were selected, based upon sequence similarities to Giardia lamblia PPDK and Zea mays PPDK. Three-dimensional (3-D) models were generated for PPDKs from divergent organisms and were used to compare the orientation of the phosphorylatable histidine residue within the central domain of PPDKs. These PPDKs were compared using a maximum-likelihood tree. RESULTS: For PPDK from Giardia, as well as from other anaerobic protozoans, the central domain tilted toward the N-terminal nucleotide-binding domain, indicating that this enzyme catalyzed ATP synthesis. Furthermore, the orientation of this central domain was determined by interactions between the N- and C-terminal domains. Phylogenetic analysis of the N- and C-terminal sequences of PPDKs from different species suggested that PPDK has likely undergone adaptive evolution in response to differences in environmental and metabolic conditions. CONCLUSION: These results suggested that PPDK in anaerobic organisms is functionally adapted to generate energy more efficiently in an anaerobic environment.

[Progress of research on parasitic adaptability of schistosome and its application value].

The larval and adult schistosomes can effectively establish the stable parasitic relationship with their final hosts and then maintain the parasitism for a long time, due to the successful adaptation to their parasitic lifestyle. This paper reviews the progress of research on parasitic adaptability of schistosomes in several respects, and demonstrates the application value of schistosomal genes related to parasitic adaptability in schistosomiasis control and exploitation of natural active molecules.

Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer.

BACKGROUND: Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. RESULTS: A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. CONCLUSIONS: Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.