Elucidation of the hierarchical structure of natural eumelanins

Eumelanin is one of the most ubiquitous pigments in living organisms and plays an important role in coloration and UV protection. Because eumelanin is highly cross-linked and insoluble in solvents, the chemical structure is still not completely known. In this study, we used atomic force microscopy, X-ray photoelectron spectroscopy and solid-state nuclear magnetic resonance (NMR) to compare intact eumelanosomes (pigment granules mostly made of eumelanin) from four phylogentically distant species: cuttlefish (Sepia officinalis) inks, black fish crow (Corvus ossifragus) feathers, iridescent wild turkey (Melleagris gallopavo) feathers and black human hair. We found that eumelanosomes from all four species are composed of subunit nanoparticles with a length of 10-60 nm, consistent with earlier observations in eumelanosomes from the sepia ink and human hair. The solid-state NMR results indicate the presence of quinone methide tautomers in all four eumelanins. We also found clear differences in the UV absorbance, the ratio of 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and protonated aryl carbon ratios in sepia eumelanin relative to the other three. This comparison of natural eumelanin across a phylogenetically broad group of organisms provides insights into the change in the eumelanin structure over the evolutionary history and enables the production of synthetic eumelanin with properties that are similar to natural eumelanin

Analysis of recent segmental duplications in the bovine genome

Background: Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (>= 1 kb in length, >= 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes. Results: In this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction. Conclusion: Our results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research

Androgen deprivation therapy and radiotherapy in intermediate-risk prostate cancer: A systematic review and meta-analysis

ObjectivesAndrogen deprivation therapy combined with radiotherapy for intermediate-risk prostate cancer is still a matter of debate. We conducted a meta-analysis to evaluate the necessity of androgen deprivation therapy combined with radiotherapy for intermediate-risk prostate cancer patients.MethodsA comprehensive literature search of articles was performed in PubMed, Embase, Cochrane library, Web of Science, Chinese National Knowledge Infrastructure, Chinese Biological Medicine, Wanfang, and VIP Databases published between February 1988 and April 2022. Studies comparing the survival of patients diagnosed with intermediate-risk prostate cancer who were treated with androgen deprivation therapy combined with radiotherapy or radiotherapy alone were included. Data were extracted and analyzed with the RevMan software (version 5.3) and the Stata software (version 17).ResultsSix randomized controlled trials and nine retrospective studies, including 6853 patients (2948 in androgen deprivation therapy combined with radiotherapy group and 3905 in radiotherapy alone group) were enrolled. Androgen deprivation therapy combined with radiotherapy did not provide an overall survival (HR 1.12, 95% CI 1.01-1.12, p=0.04) or biochemical recurrence-free survival (HR 1.23, 95% CI 1.09-1.39, P=0.001) advantage to intermediate-risk prostate cancer patients.ConclusionAndrogen deprivation therapy combined with radiotherapy did not show some advantages in terms of overall survival and biochemical recurrence-free survival and radiotherapy alone may be the effective therapy for intermediate-risk prostate cancer patients.Systematic review registrationhttps://inplasy.com/inplasy-2022-8-0095/, identifier 202280095

A decision analysis model for KEGG pathway analysis

The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying active pathways in different conditions. However, current approaches are designed to analyze a biological system assuming that each pathway is independent of the other pathways. A decision analysis model is developed in this article that accounts for dependence among pathways in time-course experiments and multiple treatments experiments. This model introduces a decision coefficient—a designed index, to identify the most relevant pathways in a given experiment by taking into account not only the direct determination factor of each Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway itself, but also the indirect determination factors from its related pathways. Meanwhile, the direct and indirect determination factors of each pathway are employed to demonstrate the regulation mechanisms among KEGG pathways, and the sign of decision coefficient can be used to preliminarily estimate the impact direction of each KEGG pathway. The simulation study of decision analysis demonstrated the application of decision analysis model for KEGG pathway analysis. A microarray dataset from bovine mammary tissue over entire lactation cycle was used to further illustrate our strategy. The results showed that the decision analysis model can provide the promising and more biologically meaningful results. Therefore, the decision analysis model is an initial attempt of optimizing pathway analysis methodology.https://doi.org/10.1186/s12859-016-1285-

Development of a growth-coupled selection platform for directed evolution of heme biosynthetic enzymes in Corynebacterium glutamicum

Heme is an important tetrapyrrole compound, and has been widely applied in food and medicine industries. Although microbial production of heme has been developed with metabolic engineering strategies during the past 20 years, the production levels are relatively low due to the multistep enzymatic processes and complicated regulatory mechanisms of microbes. Previous studies mainly adopted the strategies of strengthening precursor supply and product transportation to engineer microbes for improving heme biosynthesis. Few studies focused on the engineering and screening of efficient enzymes involved in heme biosynthesis. Herein, a growth-coupled, high-throughput selection platform based on the detoxification of Zinc-protoporphyrin IX (an analogue of heme) was developed and applied to directed evolution of coproporphyrin ferrochelatase, catalyzing the insertion of metal ions into porphyrin ring to generate heme or other tetrapyrrole compounds. A mutant with 3.03-fold increase in kcat/KM was selected. Finally, growth-coupled directed evolution of another three key enzymes involved in heme biosynthesis was tested by using this selection platform. The growth-coupled selection platform developed here can be a simple and effective strategy for directed evolution of the enzymes involved in the biosynthesis of heme or other tetrapyrrole compounds

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD. In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using quantitative real-time PCR (qPCR), all of which were successfully confirmed. Finally, qPCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study. Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.https://doi.org/10.1186/s12863-020-00884-

Guardian spirit of be (Shaman) and Culture tradition : For ongdin - taban - tnger ritual

This file provide the detailed impact direction data of selected KEGG pathway categories, subcategories and the secondary pathways from− 15 to 300 vs.− 30d in bovine mammary tissue during lactation in Table S2 (a) and (b), respectively. The numbers colored in red color are the filled data by the average of all the other impact values in this pathway, which is the missing data originally. (DOCX 35 kb

Engineering allosteric inhibition of homoserine dehydrogenase by semi-rational saturation mutagenesis screening

Allosteric regulation by pathway products plays a vital role in amino acid metabolism. Homoserine dehydrogenase (HSD), the key enzyme for the biosynthesis of various aspartate family amino acids, is subject to feedback inhibition by l-threonine and l-isoleucine. The desensitized mutants with the potential for amino acid production remain limited. Herein, a semi-rational approach was proposed to relieve the feedback inhibition. HSD from Corynebacterium glutamicum (CgHSD) was first characterized as a homotetramer, and nine conservative sites at the tetramer interface were selected for saturation mutagenesis by structural simulations and sequence analysis. Then, we established a high-throughput screening (HTS) method based on resistance to l-threonine analog and successfully acquired two dominant mutants (I397V and A384D). Compared with the best-ever reported desensitized mutant G378E, both new mutants qualified the engineered strains with higher production of CgHSD-dependent amino acids. The mutant and wild-type enzymes were purified and assessed in the presence or absence of inhibitors. Both purified mutants maintained >90% activity with 10 mM l-threonine or 25 mM l-isoleucine. Moreover, they showed >50% higher specific activities than G378E without inhibitors. This work provides two competitive alternatives for constructing cell factories of CgHSD-related amino acids and derivatives. Moreover, the proposed approach can be applied to engineering other allosteric enzymes in the amino acid synthesis pathway

Genomic Analyses Reveal Mutational Signatures and Frequently Altered Genes in Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC-signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal (<100 kb) amplifications of CBX4 and CBX8. In our combined cohort, we identified frequent inactivating mutations in AJUBA, ZNF750, and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1, in addition to known mutations. Functional analyses suggest roles for several genes (CBX4, CBX8, AJUBA, and ZNF750) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets

The Influences of Micro-Alloying Element Sn and Magnetic Field on the Microstructure Evolution of Al–Bi Immiscible Alloys

An investigation was conducted through directional solidification experiments to explore the impact of micro-alloying element Sn and a magnetic field on the solidification behavior of immiscible Al–Bi alloys, as well as the combined effect of Sn and the magnetic field. Experimental results show that the size distribution of the dispersed particles in the low-speed solidified Al–3.4 wt.%Bi alloy presents two peaks, while it only shows one peak when solidified at a relatively high speed. The addition of Sn not only can enhance the nucleation rate and the number density of the Bi-rich droplets in the sample, but also decrease the Marangoni migration velocity and the axial resultant velocity of minority phase droplets in front of the solidification interface. Thereby it promotes the formation of Al–Bi alloys with a well-dispersed microstructure. A static magnetic field with the strength of 0.2 T increases the number density of the dispersed particles and decreases the average size and the size distribution width of the dispersed particles. Under the effect of Sn addition and static magnetic field, the average radius of the dispersed particles R and the solidification velocity V0 satisfy R∝V0−1/3 when the alloy was solidified at a relatively low velocity, R and V0 satisfy R∝V0−1/2 when the alloy is solidified at a high velocity