To and fro in the archipelago: Repeated inter-island dispersal and New Guinea's orogeny affect diversification of Delias, the world's largest butterfly genus.

The world's largest butterfly genus Delias, commonly known as Jezebels, comprises ca. 251 species found throughout Asia, Australia, and Melanesia. Most species are endemic to islands in the Indo-Australian Archipelago or to New Guinea and nearby islands in Melanesia, and many species are restricted to montane habitats over 1200 m. We inferred an extensively sampled and well-supported molecular phylogeny of the group to better understand the spatial and temporal dimensions of its diversification. The remarkable diversity of Delias evolved in just ca. 15-16 Myr (crown age). The most recent common ancestor of a clade with most of the species dispersed out of New Guinea ca. 14 Mya, but at least six subsequently diverging lineages dispersed back to the island. Diversification was associated with frequent dispersal of lineages among the islands of the Indo-Australian Archipelago, and the divergence of sister taxa on a single landmass was rare and occurred only on the largest islands, most notably on New Guinea. We conclude that frequent inter-island dispersal during the Neogene-likely facilitated by frequent sea level change-sparked much diversification during that period. Many extant New Guinea lineages started diversifying 5 Mya, suggesting that orogeny facilitated their diversification. Our results largely agree with the most recently proposed species group classification system, and we use our large taxon sample to extend this system to all described species. Finally, we summarize recent insights to speculate how wing pattern evolution, mimicry, and sexual selection might also contribute to these butterflies' rapid speciation and diversification.

Prognostic and biological function value of OSBPL3 in colorectal cancer analyzed by multi-omic data analysis.

BACKGROUND: Colorectal cancer (CRC) is one of the most common malignancies in the world. This study proposes to reveal prognostic biomarkers for the prognosis and treatment of CRC patients. METHODS: Differential analysis of OSBPL3 was performed in pan-cancer, and the correlation between clinical stage and OSBPL3 was analyzed. Multiple omics analysis was used to compare the relationship between survival of patients and copy number variation, single nucleotide variant, and methylation status. Survival differences between high and low OSBPL3 expression groups were analyzed. Differentially expressed genes (DEGs) between high and low OSBPL3 expression groups were obtained, and functional enrichment analysis was implemented. Correlations between immune cells and OSBPL3 was analyzed. Drug sensitivity between the two OSBPL3 expression groups was compared. Moreover, the expression of OSBPL3 was verified by immunohistochemistry and real-time quantitative PCR. RESULTS: OSBPL3 was differentially expressed in 13 tumors and had some correlations with T and N stages. OSBPL3 expression was regulated by methylation and higher OSBPL3 expression was associated with poorer prognosis in CRC. 128 DEGs were obtained and they were mainly involved in signaling receptor activator activity, aspartate and glutamate metabolism. T cell gamma delta and T cell follicular helper were significantly different in the high and low OSBPL3 expression groups. Moreover, OSBPL3 showed negative correlations with multiple drugs. OSBPL3 was significantly upregulated in CRC samples compared to normal samples. CONCLUSIONS: A comprehensive analysis demonstrated that OSBPL3 had potential prognostic value, and guiding significance for CRC chemotherapeutic.

Physiological analysis of severe chlamydia psittaci pneumonia and clinical diagnosis after doxycycline-based treatment.

Objective: To describe the clinical spectrum of severe Chlamydia psittaci pneumonia in order to understand the disease better. Methods: Retrospective analysis was made on 31 patients with severe Chlamydia psittaci pneumonia diagnosed in ICU by next-generation sequencing of metagenome Metagenomic next-generation sequencing(mNGS) from January 2019-November 2022, including clinical characteristics, laboratory examination results, imaging characteristics, treatment, and prognosis. Results: We included 31 patients with severe Chlamydia psittaci pneumonia, 15 of whom had a history of virus exposure. There were 12 cases with multiple bacterial infections, and the common symptoms included fever (31/31,100%), dyspnea (31/31, 100%), cough (22/31, 71.0%), and myalgia (20/31, 64.5%). Laboratory data showed that white blood cells were average or slightly increased, but the levels of C-reactive protein and neutrophils were high. CT findings of the lung were consolidation (19/31, 61.3%) and pleural effusion (11/31, 35.5%). Only one lobe was involved in 11 patients (35.5%). Before diagnosis, 22 patients (71.0%) did not have atypical pathogens in their antimicrobial regimen. After diagnosis, 19 patients (61.3%) received single drug treatment, of which doxycycline or moxifloxacin were the most commonly used drugs. Among 31 patients, three died, nine improved, and nineteen were cured. Conclusion: The clinical manifestations of severe Chlamydia psittaci pneumonia are non-specific. The application of mNGS can improve the diagnostic accuracy of Chlamydia psittaci pneumonia, reduce the unnecessary use of antibiotics, and shorten the course of the disease. Doxycycline-based treatment is effective for severe chlamydia psittaci pneumonia, but it is necessary to understand the secondary bacterial infection and other complications in the course of the disease.

Identification and verification of the prognostic value of CUL7 in colon adenocarcinoma.

CUL7, a gene composed of 26 exons associated with cullin 7 protein, is also an E3 ligase that is closely related to cell senescence, apoptosis, and cell transformation and also plays an important role in human cancer. However, there is no systematic pan-cancer analysis has been performed to explore its role in prognosis and immune prediction. In this study, the expression of CUL7 in colon adenocarcinoma (COAD) was investigated to determine its prognosis value. First, based on the Cancer Genome Atlas (TCGA), Genotypic-Tissue Expression Project(GTEx), Cancer Cell Line Encyclopedias(CCLE), and TISIDB database, the potential role of CUL7 in different tumors was explored. Subsequently, the expression of CUL7 in COAD was explored and verified by Immunohistochemistry (IHC). Furthermore, the mutation frequency of CUL7 in COAD was analyzed, and the prognostic value of CUL7 in COAD was discussed. In addition, the nomogram was constructed, and its prognostic value was verified by follow-up data from Jiangmen Central Hospital. Finally, PPI network analysis explored the potential biological function of CUL7 in COAD. The results show that CUL7 is upregulated in most tumors, which is significantly associated with poor survival. At the same time, CUL7 is correlated with the clinical stage and immune landscape of various tumors. In colorectal cancer, CUL7 was overexpressed in tumor tissues by IHC with a mutation frequency of about 4%. CUL7 is an independent prognostic factor for colorectal cancer. The nomogram constructed has effective predictive performance, and external databases proved the prognostic value of CUL7. In addition, PPI network analysis showed that CUL7 was closely related to FBXW8, and further pathway enrichment analysis showed that CUL7 was mainly involved in ubiquitin-mediated proteolysis. Therefore, our study provides a comprehensive understanding of the potential role of CUL7 in different tumors, and CUL7 might be a prognostic marker for COAD.

Hsa-miR-1248 suppressed the proliferation, invasion and migration of colorectal cancer cells via inhibiting PSMD10.

BACKGROUND: Lymph node metastasis (LNM) is a critical event during the colorectal cancer (CRC) development and is indicative of poor prognosis. Identification of molecular markers of LNM may facilitate better therapeutic decision-making. METHODS: Six pairs of CRC tissues and corresponding adjacent tissues [3 pairs diagnosed as pT1N0M0 (M_Low group) and 3 pairs diagnosed as pT4N2M0 (M_High group)] collected from CRC patients who underwent surgical resection were used. MicroRNA sequencing was performed to screen differential microRNAs involved in CRC LNM. The selected microRNAs were validated in CRC tissues and cell lines using qRT-PCR. The functions of candidate hsa-miR-1248 were evaluated by CCK-8, colony formation, and Transwell assay. The binding of hsa-miR-1248 with its target PSMD10 was confirmed by luciferase activity assay, and the expression of PSMD10 in tissues was detected by droplet digital polymerase chain reaction. RESULTS: Ninety-five miRNAs were downregulated in carcinoma tissues (M_Low and M_high groups) compared with the normal group. Their expression in M_High group was significantly lower compared with M_Low group. The top 3 were hsa-miR-635, hsa-miR-1248, and hsa-miR-668-3p. After validation in tissues/cell lines, only hsa- hsa-miR-1248 was decreased in high metastatic tissues or SW620 cells compared to low metastatic tissues or SW480 cells. Hsa-miR-1248 was found to inhibit CRC cell viability, proliferation, invasion, and migration. The tumor suppressor effect of has-miR-1248 in CRC cells was attenuated or enhanced by up-regulating or down-regulating PSMD10, respectively. CONCLUSION: Hsa-miR-1248 may act as a tumor suppressor gene in CRC by targeting and inhibiting PSMD10, which provides a clue for CRC treatment.

University teachers' technology integration in teaching English as a foreign language: evidence from a case study in mainland China.

Despite the increasing use of technology in education, university teachers' perceptions and use of technology are under-explored, particularly in the context of English language classrooms in mainland China. To fill the research gap, this article reports the findings of a case study exploring university teachers' perceptions of and practices with technology as well as the challenges of technology implementation. To provide a microscopic understanding of these issues from teachers' perspective, an online survey was first distributed to all 60 English teachers at a focal university, with 35 valid surveys returned. Subsequently, nine survey respondents participated in in-depth follow-up interviews. The findings suggest that teachers used technology predominantly for teacher-centred purposes rather than for active student engagement although they had positive perceptions of technology integration. They also held critical viewpoints on the use of technology in English teaching. In addition, teachers perceived more external barriers to technology integration (e.g. insufficient technical and pedagogical training, "the Great Firewall") than internal challenges (e.g. students' lack of interest in technology). The study contributes to the understanding of university teachers' technology uptake and carries important implications for the promotion of teaching innovation and effectiveness in higher education contexts. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43545-021-00223-5.

Gankyrin as Potential Biomarker for Colorectal Cancer With Occult Liver Metastases.

The majority of occult liver metastases cannot be detected by computed tomography (CT), magnetic resonance imaging (MRI) or other traditionally morphological imaging approaches since the lesions are too small or they have not yet formed cancer nodules. Gankyrin is a small molecular protein composed of seven ankyrin domains. In this study, the expression of Gankyrin in colorectal cancer (CRC) patients with liver metastases was investigated to determine its prognosis value. Gankyrin expression in CRC patients was initially analyzed using data from The Cancer Genome Atlas (TCGA) database and bioinformatics tools. RT-qPCR, western blotting, immunohistochemistry (IHC) and transwell migration and invasion assays were then performed to verify the expression and function of Gankyrin in CRC cell line, CRC tissues and matched non-tumor tissues of clinical patients. General clinicopathological information including TNM stage as well as preoperative and postoperative imaging results were collected. The main outcome indicator was overall survival (OS), referring to the length of time from surgery to either death or the last visit. Statistical analyses included chi-squared tests, Cox analyses, progression free survival (PFS) rates and OS rates. Elevated Gankyrin expression was confirmed in CRC patients. The upregulated Gankyrin expression was positively correlated with the progression of disease and liver metastasis in CRC patients. OS analysis revealed that prognosis was worse in CRC patients with high Gankyrin expression compared to those with low expression. CRC patients with higher Gankyrin expression also had a higher risk of occult liver metastases and a lower PFS rate. Therefore, Gankyrin can be used as a potential biomarker for early diagnosis of CRC with occult liver metastasis.

Optimal examined lymph node count in node-negative colon cancer should be determined.

Background: We aimed to investigate the association between optimal examined lymph node (ELNs) and overall survival to determine the optimal cutoff point. Methods: Cox models and locally weighted scatterplot smoothing were used to fit hazard ratios and explore an optimal cutoff point based on the Chow test. Results: Overall survival increased significantly with the corresponding increase in the number of ELNs after adjusting for covariates. In Chow's test, the optimal cutoff point for node-negative colon cancer was 15, which was validated in both cohorts after controlling for confounders (Surveillance, Epidemiology, and End Results database: hazard ratio: 0.701, p < 0.001; single-center: HR: 0.563; p = 0.031). Conclusions: We conservatively suggest that the optimal number of ELNs for prognostic stratification is 15 in node-negative colon cancer.

Lay abstract Over the past 20 years, the number of examined lymph nodes (ELNs) has been an important indicator to accurately assess lymph node metastasis, and therefore, many studies have focused on exploring an optimal cutoff point to prevent missed detection of positive lymph nodes. However, in recent years, ELNs has been considered to play other key roles. In the current study, ELNs were deemed an important prognostic factor, and the minimum number of ELNs was recommended to be 15 in node-negative colon cancer via rigorous statistical methods and a large sample of data.

Naringin protects H9C2 cardiomyocytes from chemical hypoxia­induced injury by promoting the autophagic flux via the activation of the HIF­1α/BNIP3 signaling pathway.

Naringin, a natural bioflavonoid, has been shown to exert protective effects in multiple cardiovascular diseases; however, the protective effects of naringin against hypoxic/ischemia­induced myocardial are not yet fully understood. Autophagy is a vital factor involved in the pathogenesis of myocardial injury. The aim of the present study was to investigate the protective effects of naringin on H9c2 cells against chemical hypoxia [cobalt chloride (CoCl2)]­induced injury. The role of autophagy and the hypoxia­inducible factor­1α (HIF­1α)/Bcl­2/BCL2 interacting protein 3 (BNIP3) signaling pathway in the protective effects of naringin were also assessed. The results revealed that naringin pre­treatment significantly attenuated the CoCl2­induced cytotoxicity and apoptosis, and also decreased caspase­3 activity, which had been increased by CoCl2. In addition, CoCl2 increased Beclin­1 expression, enhanced the IL3B­II/IL3B­I ratio and increased p62 expression in the H9C2 cells. Treatment with 3­methyladenine (3­MA), a selective inhibitor of autophagy, also blocked CoCl2­induced cytotoxicity and apoptosis. Notably, treatment with bafilomycin A1 (Baf A1), an inhibitor of the vacuolar H+ ATPase of lysosomes, resulted in an increase in the upregulation of the LC3B­II/LC3B­I ratio, but did not further increase the LC3B­II/LC3B­I ratio compared with CoCl2 treatment. These results suggested that CoCl2 inhibited the autophagic flux, which resulted in myocardial cell damage. Furthermore, naringin pre­treatment exacerbated Beclin 1 expression and the increased IL3B­II/IL3B­I ratio, and reduced p62 expression in CoCl2­treated H9C2 cells. 3­MA and Baf A1 both reversed the protective effects of naringin against CoCl2­induced injury, indicating that naringin attenuated CoCl2­induced myocardial cell injury by the increasing autophagic flux. Moreover, naringin treatment resulted in upregulated expression levels of HIF­1α and BNIP3 in the CoCl2­treated H9C2 cells. The inhibition of the HIF­1α/BNIP3 signaling pathway using 3­(5'­hydroxymethyl­2'­furyl)­1­benzylindazole (an inhibitor of HIF­1α) prevented the effects of naringin on the autophagic flux and reversed its protective effects against CoCl2­induced injury. Taken together, these results suggest that naringin protects the H9C2 cells against CoCl2­induced injury by enhancing the autophagic flux via the activation of the HIF­1α/BNIP3 signaling pathway.

Association of tumor size with prognosis in colon cancer: A Surveillance, Epidemiology, and End Results (SEER) database analysis.

BACKGROUND: Thus far, the association of tumor size with prognosis in colon cancer has not been considered and has remained unclear. This study, therefore, aimed to investigate the association between tumor size as a continuous variable and prognosis in colon cancer using Cox models with restricted cubic splines. METHODS: Using the Surveillance, Epidemiology, and End Results database, we selected 128,369 patients with colon cancer who underwent surgery. Overall survival and colon cancer-specific survival were separately analyzed, and tumor size was separately evaluated as a continuous variable and a categorical variable. To investigate the relationship after adjusting for covariates, we used the proportional hazards models. The restricted cubic splines model was used to determine the presence of nonlinear or linear association and flexibly visualize the association. RESULTS: The adjusted covariate model showed that the hazard ratio of colon cancer rapidly increased with a tumor size of 4 cm and slowly increased with a tumor size larger than 4 cm. When tumor size was analyzed as a categorical variable, the multivariable-adjusted model demonstrated a nearly linear relationship between tumor size and hazard ratio regardless of overall survival or cancer-specific survival, and the hazard ratio of group 5 (4.1-5 cm) was nearly a turning point. Subgroup analysis with respect to lymph node metastasis showed that the relationship between tumor size and prognosis in colon cancer was evident in lymph node metastasis. CONCLUSION: There was a strong negative relationship between tumor size and prognosis in colon cancer. However, when tumor size was less than 4 cm, the relationship between tumor size and prognosis was steep compared with that when tumor size was larger than 4 cm, especially in lymph node metastasis.

High-Dose Vitamin C Tends to Kill Colorectal Cancer with High MALAT1 Expression.

BACKGROUND: Vitamin C (Vc) deficiency is frequently observed in cancer sites and has been proposed to have an antitumor effect. However, the mechanism of Vc's killing effect is not clear. Besides, epigenetic alterations exhibit significant effects on colorectal cancer (CRC). This study aimed to explore the mechanism of Vc's killing effect and its association to epigenetic alterations in CRC. METHODS: Cell morphology, apoptosis, proliferation, and cycle were assayed to test Vc's suppressive function in CRC cell lines. Xenograft and peritoneal implantation metastasis models were performed to evaluate the high-dose Vc's inhibitory effect on tumor growth and metastasis. Immunohistochemistry was used to measure CD31 expression in solid tumors. A literature summary was applied for screening differently expressed long noncoding RNAs (lncRNAs) in CRC tissues and was closely associated with CRC progression. The qPCR was used to detect the expression of these lncRNAs. The association between Vc and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) was evaluated in MALAT1-transfected CRC cells and a xenograft model. RESULTS: Vc was confirmed to function in proliferation suppression, apoptosis induction, and S phase arresting in CRC cell lines. High-dose Vc, but not physiologically low-dose Vc, was identified as a suppressive function on tumor growth in xenograft models and an inhibitory effect on implantation metastasis in peritoneal implantation metastasis mice. Furthermore, a consistent downregulation of MALAT1 induced by Vc was verified among CRC cell lines and tumor tissues from both mouse models. Finally, experiments on MALAT1-knockdown CRC cells and its xenograft model suggested that Vc had a tendency in killing CRC with high MALAT1 expression. CONCLUSIONS: Our findings demonstrate that high-dose Vc has more efficiency in suppressing CRC with higher MALAT1 expression. It gives high-dose Vc the possibility of a better curative effect on CRC with overexpressed MALAT1. Further clinical studies are still needed.

Development and evaluation of a WebQuest-based teaching programme: Students' use of exploratory talk to exercise critical thinking.

This article reports the findings of an exploratory study involving the development and implementation of a WebQuest-based critical-thinking programme in Hong Kong primary English classrooms. Using 'design research' as its methodological framework, the study investigated the critical-thinking performance of 125 primary school students. Sociocultural discourse analysis of classroom dialogue during programme implementation revealed the participating students to have engaged in explicit reasoning and used 'exploratory talk' as a dialogic tool in exercising critical thinking. The study has profound implications for pedagogical practice with respect to the use of educational technology for critical-thinking cultivation. This article thus makes significant contributions to the WebQuest and critical-thinking literature, extending it to the Hong Kong language education context and beyond.

Survival outcome of palliative primary tumor resection for colorectal cancer patients with synchronous liver and/or lung metastases: A retrospective cohort study in the SEER database by propensity score matching analysis.

BACKGROUND: There is a great matter of controversies whether some of these synchronous metastatic colorectal cancer patients can benefit from palliative primary tumor resection (pPTR) and there is still no reported randomized control trial to address this issue. METHODS: Patients with microscopically proven metastatic colorectal cancer were identified within the SEER database (2010-2016). Patients were propensity matched 1:1 into pPTR and non-surgery groups and among the matched cohort, the univariable and multivariable Cox proportional hazards regression models were performed to identify predictors of survival. Median survival was calculated by using the Kaplan-Meier method. RESULTS: Of 21,405 colorectal cancer patients diagnosed with synchronous liver and/or lung metastases, 7386 were identified in the matched cohort. The median overall survival was 12.0 months, 22.0 months in the non-surgery, surgery groups, respectively (p < 0.001) and the corresponding median cancer-specific survival was 13.0 months, 22.0 months, respectively (p < 0.001). Multivariable Cox regression analysis demonstrated that surgery was independently associated with improved overall survival (hazard ratio, 0.531) as well as cancer-specific survival (hazard ratio, 0.516). In stratified analyses by primary site and patterns of distant metastases, those patients with pPTR had better prognosis. In addition, stratified analysis revealed that trimodality therapy was linked with the greatest therapeutic effect followed by addition of chemotherapy to pPTR. CONCLUSIONS: pPTR may offer some therapeutic benefits among carefully selected patients, and surgery-based multimodality therapy was associated with better survival.

Anti-TGF-ß attenuates tumor growth via polarization of tumor associated neutrophils towards an anti-tumor phenotype in colorectal cancer.

Tumor associated neutrophils (TANs) play important roles in the progress of CRC. Since tumor microenvironments could influence the phenotypes of TANs, altering the tumor microenvironment to polarize the phenotype of TANs may be a new strategy for tumor treatment. This study aims to investigate the effect of anti-TGF-ß on the polarization of TANs from a pro-tumor phenotype towards an anti-tumor phenotype in CRC. In this work, CRC patients had more infiltration of TANs and higher expression of TGF-ß in CRC tissue when compared with the controls. In vitro, SW480 cells were co-cultured with primed neutrophils, which simulated the TANs in the tumor microenvironment, and TGF-ß was blocked by anti-TGF-ß (1D11) in order to polarize TANs. Anti-TGF-ß treatment increased the cytotoxicity of TANs and decreased the metastatic chemoattractants secreted by TANs, and ultimately increased the apoptosis of CRC cells significantly while remarkably suppressing the migration of tumor cells. The changes of signaling pathways in the TANs and tumor cells were explored. The results showed that anti-TGF-ß attenuated CRC may be partly mediated by suppression of PI3K/AKT signaling pathways in TANs and partly mediated by suppression of TGF-ß/Smad signaling pathways in tumor cells. Furthermore, the tumor in the mice treated with 1D11 was obviously smaller and had reverse tumorigenesis compared with the controls, while neutrophil depletion reduced the anti-tumor effect of 1D11. Our data suggest that anti-TGF-ß attenuates tumor growth via the polarization of TANs to an anti-tumor phenotype in CRC, which provides new strategies for CRC treatment.

Long non-coding RNA MALAT1 sponges miR-149 to promote inflammatory responses of LPS-induced acute lung injury by targeting MyD88.

Acute lung injury (ALI) caused by sepsis occurs early and the condition is severe, and is also an important reason for accelerating the death of patients. Increasing evidence has identified long non-coding RNA (lncRNA) metastasis associated in lung adenocarcinoma transcript 1 (MALAT1) as a regulator of ALI. However, the potential mechanism underlying MALAT1 on ALI still needs further identification. To explore the mechanisms of gene regulation expression mediated by MALAT1 through miR-149/MyD88 in lung injury inflammation, we constructed a lung injury inflammatory model using the lipopolysaccharides (LPS)-induced method and quantificated the cytokines and signaling cascade molecules as well as miR-149. The MALAT1, myeloid differentiation factor 88 (MyD88), tumor necrosis factor-α (TNF-α), interleukin-1ß (IL-1ß), and IL-6 levels were significantly increased, and the nuclear factor-κB (NF-κB) pathway was activated, but the miR-149 level was decreased in the LPS-induced ALI model. miR-149 directly targeted both lncRNA MALAT1 and the MyD88 gene. Knockdown of MALAT1 down-regulated the levels of MyD88, TNF-α, IL-1ß, and IL-6, and inhibited the NF-κB pathway. However, MALAT1 knockdown up-regulated the expression of miR-149. Overexpression of miR-149 down-regulated MyD88, TNF-α, IL-1ß, and IL-6 levels, and inhibited the NF-κB pathway. MALAT1 acts as a pro-inflammatory factor in ALI via the miR-149/MyD88/NF-κB axis and is therefore a potential novel therapeutic target for ALI treatment.

An in vitro DNA phosphorothioate modification reaction.

Phosphorothioation (PT) involves the replacement of a nonbridging phosphate oxygen on the DNA backbone with sulfur. In bacteria, the procedure is both sequence- and stereo-specific. We reconstituted the PT reaction using purified DndCDE from Salmonella enterica and IscS from Escherichia coli. We determined that the in vitro process of PT was oxygen sensitive. Only one strand on a double-stranded (ds) DNA substrate was modified in the reaction. The modification was dominant between G and A in the GAAC/GTTC conserved sequence. The modification between G and T required the presence of PT between G and A on the opposite strand. Cysteine, S-adenosyl methionine (SAM) and the formation of an iron-sulfur cluster in DndCDE (DndCDE-FeS) were essential for the process. Results from SAM cleavage reactions support the supposition that PT is a radical SAM reaction. Adenosine triphosphate (ATP) promoted the reaction but was not essential. The data and conclusions presented suggest that the PT reaction in bacteria involves three steps. The first step is the binding of DndCDE-FeS to DNA and searching for the modification sequence, possibly with the help of ATP. Cysteine locks DndCDE-FeS to the modification site with an appropriate protein conformation. SAM triggers the radical SAM reaction to complete the oxygen-sulfur swapping.

Conservation of genetic uniqueness in remaining populations of red squirrels (Sciurus vulgaris L.) in the South of England.

The Eurasian red squirrel (Sciurus vulgaris) is an emblematic species for conservation, and its decline in the British Isles exemplifies the impact that alien introductions can have on native ecosystems. Indeed, red squirrels in this region have declined dramatically over the last 60 years due to the spread of squirrelpox virus following the introduction of the gray squirrel (Sciurus carolinensis). Currently, red squirrel populations in Britain are fragmented and need to be closely monitored in order to assess their viability and the effectiveness of conservation efforts. The situation is even more dramatic in the South of England, where S. vulgaris survives only on islands (Brownsea Island, Furzey Island, and the Isle of Wight). Using the D-loop, we investigated the genetic diversity and putative ancestry of the squirrels from Southern England and compared them to a European dataset composed of 1,016 samples from 54 populations. We found that our three populations were more closely related to other squirrels from the British Isles than squirrels from Europe, showed low genetic diversity, and also harbored several private haplotypes. Our study demonstrates how genetically unique the Southern English populations are in comparison with squirrels from the continental European range. We report the presence of four private haplotypes, suggesting that these populations may potentially harbor distinct genetic lineages. Our results emphasize the importance of preserving these isolated red squirrel populations for the conservation of the species.

Effect of Hydrophobic Interactions on Lower Critical Solution Temperature for Poly(N-isopropylacrylamide-co-dopamine Methacrylamide) Copolymers.

For the preparation of thermoresponsive copolymers, for e.g., tissue engineering scaffolds or drug carriers, a precise control of the synthesis parameters to set the lower critical solution temperature (LCST) is required. However, the correlations between molecular parameters and LCST are partially unknown and, furthermore, LCST is defined as an exact temperature, which oversimplifies the real situation. Here, random N-isopropylacrylamide (NIPAM)/dopamine methacrylamide (DMA) copolymers were prepared under a systematical variation of molecular weight and comonomer amount and their LCST in water studied by calorimetry, turbidimetry, and rheology. Structural information was deduced from observed transitions clarifying the contributions of molecular weight, comonomer content, end-group effect or polymerization degree on LCST, which were then statistically modeled. This proved that the LCST can be predicted through molecular structure and conditions of the solutions. While the hydrophobic DMA lowers the LCST especially the onset, polymerization degree has an important but smaller influence over all the whole LCST range.

Determination of genetic associations between indels in 11 candidate genes and milk composition traits in Chinese Holstein population.

BACKGROUND: We have previously identified 11 promising candidate genes for milk composition traits by resequencing the whole genomes of 8 Holstein bulls with extremely high and low estimated breeding values for milk protein and fat percentages (high and low groups), including FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH those contained 25 indels between high and low groups. In this study, the purpose was to further examine whether these candidates have significant genetic effects on milk protein and fat traits. RESULTS: With PCR product sequencing, 13 indels identified by whole genome resequencing were successfully genotyped. With association analysis in 769 Chinese Holstein cows, we found that the indel in FCGR2B was significantly associated with milk yield, protein yield and protein percentage (P = 0.0041 to 0.0297); five indels in CENPE and one indel in MAP3K1 were markedly relevant to milk yield, fat yield and protein yield (P < 0.0001 to 0.0073); polymorphism in RETSAT was evidently associated with milk yield, fat yield, protein yield and protein percentage (P = 0.0001 to 0.0237); variant in ACSBG2 affected fat yield and protein percentage (P = 0.0088 and 0.0052); one indel in TBC1D1 was with respect to fat percentage and protein percentage (P = 0.0224 and 0.0209). Significant associations were shown between indels in NLK and protein yield and protein percentage (P = 0.0012 to 0.0257); variant in UGDH was related to the milk yield (P = 0.0312). The two exonic indels in FCGR2B and CENPE were predicted to change the mRNA and protein secondary structures, and resulted in the corresponding protein dysfunction. CONCLUSION: Our findings presented here provide the first evidence for the associations of eight functional genes with milk yield and composition traits in dairy cattle.

Phosphorothioated DNA Is Shielded from Oxidative Damage.

DNA is the carrier of genetic information. DNA modifications play a central role in essential physiological processes. Phosphorothioation (PT) modification involves the replacement of an oxygen atom on the DNA backbone with a sulfur atom. PT modification can cause genomic instability in Salmonella enterica under hypochlorous acid stress. This modification restores hydrogen peroxide (H2O2) resistance in the catalase-deficient Escherichia coli Hpx- strain. Here, we report biochemical characterization results for a purified PT modification protein complex (DndCDE) from S. enterica We observed multiplex oligomeric states of DndCDE by using native PAGE. This protein complex bound avidly to PT-modified DNA. DndCDE with an intact iron-sulfur cluster (DndCDE-FeS) possessed H2O2 decomposition activity, with a Vmax of 10.58 ± 0.90 mM min-1 and a half-saturation constant, K0.5S, of 31.03 mM. The Hill coefficient was 2.419 ± 0.59 for this activity. The protein's activity toward H2O2 was observed to be dependent on the intact DndCDE and on the formation of an iron-sulfur (Fe-S) cluster on the DndC subunit. In addition to cysteine residues that mediate the formation of this Fe-S cluster, other cysteine residues play a catalytic role. Finally, catalase activity was also detected in DndCDE from Pseudomonas fluorescens Pf0-1. The data and conclusions presented suggest that DndCDE-FeS is a short-lived catalase. Our experiments also indicate that the complex binds to PT sites, shielding PT DNA from H2O2 damage. This catalase shield might be able to extend from PT sites to the entire bacterial genome.IMPORTANCE DNA phosphorothioation has been reported in many bacteria. These PT-hosting bacteria live in very different environments, such as the human body, soil, or hot springs. The physiological function of DNA PT modification is still elusive. A remarkable property of PT modification is that purified genomic PT DNA is susceptible to oxidative cleavage. Among the oxidants, hypochlorous acid and H2O2 are of physiological relevance for human pathogens since they are generated during the human inflammation response to bacterial infection. However, expression of PT genes in the catalase-deficient E. coli Hpx- strain restores H2O2 resistance. Here, we seek to solve this obvious paradox. We demonstrate that DndCDE-FeS is a short-lived catalase that binds tightly to PT DNA. It is thus possible that by docking to PT sites the catalase activity protects the bacterial genome against H2O2 damage.