Construction of an American mink Bacterial Artificial Chromosome (BAC) library and sequencing candidate genes important for the fur industry

<p>Abstract</p> <p>Background</p> <p>Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects.</p> <p>Results</p> <p>Here, we report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (<it>Neovison vison</it>). The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs), representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library. These included candidate genes for coat coloring, hair growth and length, coarseness, and some receptors potentially involved in viral diseases in mink. The extensive screening yielded positive results for 19 of these genes. Thirty-five clones corresponding to 19 genes were sequenced using 454 Roche, and large contigs (184 kb in average) were assembled. Knowing the complete sequences of these candidate genes will enable confirmation of the association with a phenotype and the finding of causative mutations for the targeted phenotypes.</p> <p>Additionally, 1577 BAC clones were end sequenced; 2505 BAC end sequences (80% of BACs) were obtained. An excess of 2 Mb has been analyzed, thus giving a snapshot of the mink genome.</p> <p>Conclusions</p> <p>The availability of the CHORI-321 American mink BAC library will aid in identification of genes and genomic regions of interest. We have demonstrated how the library can be used to identify specific genes of interest, develop genetic markers, and for BAC end sequencing and deep sequencing of selected clones. To our knowledge, this is the first report of 454 sequencing of selected BAC clones in mammals and re-assures the suitability of this technique for obtaining the sequence information of genes of interest in small genomics projects. The BAC end sequences described in this paper have been deposited in the GenBank data library [<ext-link ext-link-id="HN339419" ext-link-type="gen">HN339419</ext-link>-<ext-link ext-link-id="HN341884" ext-link-type="gen">HN341884</ext-link>, <ext-link ext-link-id="HN604664" ext-link-type="gen">HN604664</ext-link>-<ext-link ext-link-id="HN604702" ext-link-type="gen">HN604702</ext-link>]. The 454 produced contigs derived from selected clones are deposited with reference numbers [GenBank: <ext-link ext-link-id="JF288166" ext-link-type="gen">JF288166</ext-link>-<ext-link ext-link-id="JF288183" ext-link-type="gen">JF288183</ext-link> &<ext-link ext-link-id="JF310744" ext-link-type="gen">JF310744</ext-link>].</p

UV-triggered dopamine polymerization: Control of polymerization, surface coating, and photopatterning

UV irradiation is demonstrated to initiate dopamine polymerization and deposition on different surfaces under both acidic and basic pH. The observed acceleration of the dopamine polymerization is explained by the UV-induced formation of reactive oxygen species that trigger dopamine polymerization. The UV-induced dopamine polymerization leads to a better control over polydopamine deposition and formation of functional polydopamine micropatterns

Abnormal phenomena in a one-dimensional periodic structure containing left-handed materials

The explicit dispersion equation for a one-dimensional periodic structure with alternative layers of left-handed material (LHM) and right-handed material (RHM) is given and analyzed. Some abnormal phenomena such as spurious modes with complex frequencies, discrete modes and photon tunnelling modes are observed in the band structure. The existence of spurious modes with complex frequencies is a common problem in the calculation of the band structure for such a photonic crystal. Physical explanation and significance are given for the discrete modes (with real values of wave number) and photon tunnelling propagation modes (with imaginary wave numbers in a limited region).Comment: 10 pages, 4 figure

A pair of gametologous genes provides further insights into avian comparative cytogenomics

Exploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative cytogenomic studies. Using bioinformatic, molecular (overgo BAC library scanning), and cytogenetic (BAC-based FISH) techniques, we have investigated in detail a pair of UBE2R2/UBE2R2L gametologs. By screening a gridded genomic jungle fowl BAC library, CHORI-261, with a short labeled UBE2R2L gene fragment called overgo probe, we detected seven specific clones. For three of them, CH261-019I23, CH261-105E16, and CH261-114G22, we identified their precise cytogenetic location on the Gallus gallus W chromosome (GGAW). They also co-localized with the UBAP2L2 gene on the, as was shown previously, along with the CH261-053P09 BAC clone also containing the GGAW-specific UBE2R2L DNA sequence. The fine mapping of the UBE2R2/UBE2R2L homologs in the chicken genome also shed the light on comparative cytogenetic aspects in birds. Our findings provided further evidence that bird genomes moderately changed only during evolution and are suitable for successful use of interspecies hybridization using both overgo-based BAC library screen and BAC-based FISH

Correction to: A pair of gametologous genes provides further insights into avian comparative cytogenomics

Biologia https://doi.org/10.1007/s11756-023-01395-6 The original article has been updated to reflect added changes in the list of references. The original article has been corrected

Identifying amyloid pathology–related cerebrospinal fluid biomarkers for Alzheimer\u27s disease in a multicohort study

Introduction: The dynamic range of cerebrospinal fluid (CSF) amyloid β (Aβ1–42) measurement does not parallel to cognitive changes in Alzheimer\u27s disease (AD) and cognitively normal (CN) subjects across different studies. Therefore, identifying novel proteins to characterize symptomatic AD samples is important. Methods: Proteins were profiled using a multianalyte platform by Rules Based Medicine (MAP-RBM). Due to underlying heterogeneity and unbalanced sample size, we combined subjects (344 AD and 325 CN) from three cohorts: Alzheimer\u27s Disease Neuroimaging Initiative, Penn Center for Neurodegenerative Disease Research of the University of Pennsylvania, and Knight Alzheimer\u27s Disease Research Center at Washington University in St. Louis. We focused on samples whose cognitive and amyloid status was consistent. We performed linear regression (accounted for age, gender, number of apolipoprotein E (APOE) e4 alleles, and cohort variable) to identify amyloid-related proteins for symptomatic AD subjects in this largest ever CSF–based MAP-RBM study. ANOVA and Tukey\u27s test were used to evaluate if these proteins were related to cognitive impairment changes as measured by mini-mental state examination (MMSE). Results: Seven proteins were significantly associated with Aβ1–42 levels in the combined cohort (false discovery rate adjusted P \u3c .05), of which lipoprotein a (Lp(a)), prolactin (PRL), resistin, and vascular endothelial growth factor (VEGF) have consistent direction of associations across every individual cohort. VEGF was strongly associated with MMSE scores, followed by pancreatic polypeptide and immunoglobulin A (IgA), suggesting they may be related to staging of AD. Discussion: Lp(a), PRL, IgA, and tissue factor/thromboplastin have never been reported for AD diagnosis in previous individual CSF–based MAP-RBM studies. Although some of our reported analytes are related to AD pathophysiology, other\u27s roles in symptomatic AD samples worth further explorations