Applying Cytogenetics in Phylogenetic Studies

Cytogenetics, with its fundamental role in the field of genetic investigation, continues to be an indispensable tool for studying phylogenetics, given that currently molecular evolutionary analyses are more commonly utilized. Chromosomal evolution indicated that genomic evolution occurs at the level of chromosomal segments, namely, the genomic blocks in the size of Mb‐level. The recombination of homologous blocks, through the mechanisms of insertion, translocation, inversion, and breakage, has been proven to be a major mechanism of speciation and subspecies differentiation. Meanwhile, molecular cytogenetics (fluorescence in situ hybridization‐based methodologies) had been already widely applied in studying plant genetics since polyploidy is common in plant evolution and speciation. It is now recognized that comparative cytogenetic studies can be used to explore the plausible phylogenetic relationships of the extant mammalian species by reconstructing the ancestral karyotypes of certain lineages. Therefore, cytogenetics remains a feasible tool in the study of comparative genomics, even in this next generation sequencing (NGS) prevalent era

Species and sex comparisons of karyotype and genome size in two <em>Kurixalus tree</em> frogs (Anura, Rhacophoridae)

Kurixalus is a rhacophorid genus of tree frogs that are similar in morphology but vary in reproductive behavior. We investigated the cytogenetic features and genome size using conventional G-banding, C-banding and silver-staining techniques, fluorescence in situ hybridization (FISH), and flow cytometry in two representatives of Kurixalus (K. eiffingeri Boettger, 1895 and K. idiootocus Kuramoto and Wang, 1987) and compared the data between species and sex. The two Kurixalus species share a diploid chromosome number 2n = 26 and fundamental number FN = 52. Prominent differences between species were noted in the distribution of secondary constriction (SC)/nucleolus organizer region (NOR) and dense heterochromatin. Other interspecies differences including variations in the number of metacentric and submetacentric chromosomes and staining intensity of heterochromatin were also found. The cytogenetic results are consistent with the observed differences in their genome sizes. FISH with telomeric motif (TTAGGG)n for both species detected signals in the terminal regions. Intersex comparisons revealed no differences in terms of cytogenetic features and genome size in the two species. Despite the apparent highly conserved diploid chromosome number, data on the karyotype microstructure characterize the cytogenetic profile of the two Kurixalus species that contribute to clarification of the chromosomal homologies and the rearrangement mechanisms occurring during the karyotype evolution of Kurixalus. No heteromorphic chromosome pair in both species is consistent with the view that homomorphic sex chromosome is common in amphibians

Multicolor emission based on a N, N′—Disubstituted dihydrodibenzo [a, c] phenazine crown ether macrocycle

Dynamic fluorophore 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine (DPAC) affords a new platform to produce diverse emission outputs. In this paper, a novel DPAC-containing crown ether macrocycle D-6 is synthesized and characterized. Host-guest interactions of D-6 with different ammonium guests produced a variety of fluorescence with hypsochromic shifts up to 130 nm, which are found to be affected by choice of solvent or guest and host/guest stoichiometry. Formation of supramolecular complexes were confirmed by UV-vis titration, 1H NMR and HRMS spectroscopy

Motorized Macrocycle:A Photo-responsive Host with Switchable and Stereoselective Guest Recognition

Designing photo-responsive host–guest systems can provide versatile supramolecular tools for constructing smart systems and materials. We designed photo-responsive macrocyclic hosts, modulated by light-driven molecular rotary motors enabling switchable chiral guest recognition. The intramolecular cyclization of the two arms of a first-generation molecular motor with flexible oligoethylene glycol chains of different lengths resulted in crown-ether-like macrocycles with intrinsic motor function. The octaethylene glycol linkage enables the successful unidirectional rotation of molecular motors, simultaneously allowing the 1:1 host–guest interaction with ammonium salt guests. The binding affinity and stereoselectivity of the motorized macrocycle can be reversibly modulated, owing to the multi-state light-driven switching of geometry and helicity of the molecular motors. This approach provides an attractive strategy to construct stimuli-responsive host–guest systems and dynamic materials

CLDN5 affects lncRNAs acting as ceRNA dynamics contributing to regulating blood-brain barrier permeability in tumor brain metastasis

The blood‑brain barrier (BBB) constitutes an efficient organization of tight junctions that limits the delivery of tumor to the brain. The principal tight junction protein in BBB is claudin‑5 (CLDN5), but its mechanism of action remains largely unknown. Long non‑coding RNAs (lncRNAs) are aberrantly expressed in many cancers, some lncRNAs play key roles in regulating BBB permeability and are involved in tumor brain metastasis. In particular, lncRNAs can function as competing endogenous RNAs (ceRNAs). Herein, we investigated whether ceRNA dysregulation is associated with alterations of the level of CLDN5 in human brain vascular endothelial hCMEC/D3 cells. The Affymetrix Human Transcriptome Array 2.0 and Affymetrix GeneChip miRNA 4.0 Array were used to detect the expression levels of 2,578 miRNAs, 22,829 lncRNAs, and 44,699 mRNAs in pLL3.7‑CLDN5‑transfected and pLL3.7 control hCMEC/D3 cells. The distinctly expressed miRNAs, lncRNAs, and mRNAs were subjected to construction of miRNA‑lncRNA‑mRNA interaction network. A total of 41 miRNAs, 954 lncRNAs, and 222 mRNAs were found to be differentially expressed between the CLDN5‑overexpressing and control group. 148 lncRNA acting as ceRNAs were identified based on the miRNA‑lncRNA‑mRNA interaction network. The function of differential mRNA in the network was determined by GO and pathway analysis. The potential roles of the 27 ceRNAs were revealed, the possible biology functions of these regulatory ceRNAs mainly included tight junction, focal adhesion, cell‑cell adhesion, cell growth and apoptosis. The identified sets of miRNAs, lncRNAs and mRNAs specific to CLDN5‑overexpressing hCMEC/D3 cells were verified by quantitative real‑time RT‑PCR experiment. Our study predicts the biological functions of a multitude of ceRNAs associated with the alteration of CLDN5 in brain vascular endothelial cells. Our data suggest that these dysregulated ceRNAs, in conjunction with the high CLDN5 levels, could serve as useful targets of prevention of brain metastasis formation. Further studies are warranted to determine the role of these ceRNAs in facilitating the function of CLDN5 in brain‑tumor barrier

Sublethal Doses of Anthrax Lethal Toxin on the Suppression of Macrophage Phagocytosis

BACKGROUND: Lethal toxin (LT), the major virulence factor produced by Bacillus anthracis, has been shown to suppress the immune system, which is beneficial to the establishment of B. anthracis infections. It has been suggested that the suppression of MEK/MAPK signaling pathways of leukocytes contributes to LT-mediated immunosuppressive effects. However, the involvement of MAPK independent pathways has not been clearly elucidated; nor has the crucial role played by LT in the early stages of infection. Determining whether LT exerts any pathological effects before being enriched to an MEK inhibitory level is an important next step in the furtherance of this field. METHODOLOGY/PRINCIPAL FINDINGS: Using a cell culture model, we determined that low doses of LT inhibited phagocytosis of macrophages, without influencing MAPK pathways. Consistent low doses of LT significantly suppressed bacterial clearance and enhanced the mortality of mice with bacteremia, without suppressing the MEK1 of splenic and peripheral blood mononuclear cells. CONCLUSION/SIGNIFICANCE: These results suggest that LT suppresses the phagocytes in a dose range lower than that required to suppress MEK1 in the early stages of infection

Genome-Wide Gene Expression Analysis Implicates the Immune Response and Lymphangiogenesis in the Pathogenesis of Fetal Chylothorax

Fetal chylothorax (FC) is a rare condition characterized by lymphocyte-rich pleural effusion. Although its pathogenesis remains elusive, it may involve inflammation, since there are increased concentrations of proinflammatory mediators in pleural fluids. Only a few hereditary lymphedema-associated gene loci, e.g. VEGFR3, ITGA9 and PTPN11, were detected in human fetuses with this condition; these cases had a poorer prognosis, due to defective lymphangiogenesis. In the present study, genome-wide gene expression analysis was conducted, comparing pleural and ascitic fluids in three hydropic fetuses, one with and two without the ITGA9 mutation. One fetus (the index case), from a dizygotic pregnancy (the cotwin was unaffected), received antenatal OK-432 pleurodesis and survived beyond the neonatal stage, despite having the ITGA9 mutation. Genes and pathways involved in the immune response were universally up-regulated in fetal pleural fluids compared to those in ascitic fluids. Furthermore, genes involved in the lymphangiogenesis pathway were down-regulated in fetal pleural fluids (compared to ascitic fluid), but following OK-432 pleurodesis, they were up-regulated. Expression of ITGA9 was concordant with overall trends of lymphangiogenesis. In conclusion, we inferred that both the immune response and lymphangiogenesis were implicated in the pathogenesis of fetal chylothorax. Furthermore, genome-wide gene expression microarray analysis may facilitate personalized medicine by selecting the most appropriate treatment, according to the specific circumstances of the patient, for this rare, but heterogeneous disease

Preoperative serum carcinoembryonic antigen, albumin and age are supplementary to UICC staging systems in predicting survival for colorectal cancer patients undergoing surgical treatment

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to determine influence of prognostic factors in addition to UICC staging systems, on cancer-specific and overall survival rates for patients with colorectal cancer (CRC) undergoing surgical treatment.</p> <p>Methods</p> <p>Between January 1996 and December 2006, a total of 1367 CRC patients who underwent surgical treatment in Kaohsiung Medical University Hospital were analyzed. We retrospectively investigated clinicopathologic features of these patients. All patients were followed up intensively, and their outcomes were investigated completely.</p> <p>Results</p> <p>Of 1367 CRC patients, there were seven hundred and fifty-seven males (55.4%) and 610 (44.6%) females. The median follow-up period was 60 months (range, 3–132 months). A multivariate analysis identified that low serum albumin level (<it>P </it>= 0.011), advanced UICC stage (<it>P </it>< 0.001), and high carcinoembryonic antigen (CEA) level (<it>P </it>< 0.001) were independent prognostic factors of cancer-specific survival. Meanwhile, a multivariate analysis showed age over 65 years (<it>P </it>< 0.001), advanced UICC stage (<it>P </it>< 0.001), and high CEA level (<it>P </it>< 0.001) were independent prognostic factors of overall survival. Furthermore, combination of UICC stage, serum CEA and albumin levels as predictors of cancer-specific survival showed that the poorer the prognostic factors involved, the poorer the cancer-specific survival rate. Likewise, combination of UICC stage, age and serum CEA level as predictors of overall survival showed that the poorer the prognostic factors involved, the poorer the overall survival rate. Of these prognostic factors, preoperative serum CEA level was the only significant prognostic factor for patients with stage II and III CRCs in both cancer-specific and overall survival categories.</p> <p>Conclusion</p> <p>Preoperative serum albumin level, CEA level and age could prominently affect postoperative outcome of CRC patients undergoing surgical treatment. In addition to conventional UICC staging system, it might be imperative to take these additional characteristics of factors into account in CRC patients prior to surgical treatment.</p