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Bird species present in urban parks are more colorful than urban avoiders:A test in the Argentinian Pampas

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Avian Research 2024年第1期15卷 22-26页

作者： Lucas M.Leveau Departamento de Ecología Genetica y EvolucionFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires-IEGEBA(CONICET-UBA)Intendente Güiraldes 2160Ciudad UniversitariaC1428EGABuenos AiresArgentina

Bird plumage color has been assessed as a possible trait driving the presence of bird species in urban *** some species can see the ultraviolet(UV) spectrum,the mentioned studies did not take into account UV reflectance when characterizing bird *** study aimed to use a recent database of the colorfulness in passerines that incorporated the UV spectrum to compare bird colorfulness and other traits between urban parks and rural areas in Central-East *** in urban parks were surveyed in 51 parks in 6 cities during breeding and non-breeding seasons.A list of Passeriformes species from parks was created,and a list of urban avoider species was created from the *** traits were body mass,clutch size,migratory status,nesting site,diet and habitat breadth,and plumage colorfulness.A total of 85 species were detected in the regional pool,of which 30 species were detected in urban *** species present in urban parks were more colorful than bird species only present in rural *** addition,bird presence in urban parks was positively related to their regional frequency and diet ***,urban presence was related to nesting on trees and buildings,whereas species not present in urban parks nested on the *** results obtained showed that bird color is significantly associated with presence of bird species in urban parks.

关键词： Avian Filter Phenotype Selection Ultraviolet

NK2 homeobox gene cluster: Functions and roles in human diseases

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Genes & Diseases 2023年第5期10卷 2038-2048页

作者： Catia Mio Federica Baldan Giuseppe Damante Dipartimento di Area Medica Universitàdegli Studi di UdineUdine 33100Italy Istituto di genetica Medica Azienda Sanitaria Universitaria Friuli CentraleUdine 33100Italy

NK2 genes (NKX2 gene cluster in humans) encode for homeodomain-containing transcription factors that are conserved along the phylogeny. According to the most detailed classifications, vertebrate NKX2 genes are classified into two distinct families, NK2.1 and NK2.2 . The former is constituted by NKX2-1 and NKX2-4 genes, which are homologous to the Drosophila scro gene;the latter includes NKX2-2 and NKX2-8 genes, which are homologous to the Drosophila vnd gene. Conservation of these genes is not only related to molecular structure and expression, but also to biological functions. In Drosophila and vertebrates, NK2 genes share roles in the development of ventral regions of the central nervous system. In vertebrates, NKX2 genes have a relevant role in the development of several other organs such as the thyroid, lung, and pancreas. Loss-of-function mutations in NKX2-1 and NKX2-2 are the monogenic cause of the brain-lung-thyroid syndrome and neonatal diabetes, respectively. Alterations in NKX2-4 and NKX2-8 genes may play a role in multifactorial diseases, autism spectrum disorder, and neural tube defects, respectively. NKX2-1 , NKX2-2 , and NKX2-8 are expressed in various cancer types as either oncogenes or tumor suppressor genes. Several data indicate that evaluation of their expression in tumors has diagnostic and/or prognostic value.

关键词： Drosophila melanogaster Evolutionary conservation Homeobox Homeotic genes NK2 genes

Metastasis-associated lung adenocarcinoma transcript 1 molecular mechanisms in gastric cancer progression

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World Journal of Gastrointestinal Oncology 2023年第9期15卷 1520-1530页

作者： Daniel Mateus de Oliveira Batista Jessica Manoelli Costa da Silva Carolina de Oliveira Gigek Marilia de Arruda Cardoso Smith Paulo Pimentel de Assumpcao Danielle Queiroz Calcagno Nucleo de Pesquisas em Oncologia Universidade Federal do ParaBelem 66073-000ParaBrazil Departamento de Patologia Universidade Federal de São PauloSao Paulo 04023-062São PauloBrazil Disciplina de genetica Departamento de Morfologia e GeneticaUniversidade Federal de São PauloSão Paulo 04023-900Sao PauloBrazil

Gastric cancer(GC)remains among the most common cancers worldwide with a high mortality-to-incidence *** evidence suggests that long noncoding RNAs(lncRNAs)are involved in gastric *** transcripts are longer than 200 nucleotides and modulate gene expression at multiple molecular levels,inducing or inhibiting biological processes and ***-associated lung adenocarcinoma transcript 1(MALAT1)is one of the best-studied lncRNAs with comprehensive actions contributing to cancer *** lncRNA regulates gene expression at the transcriptional and posttranscriptional levels through interactions with microRNAs and *** the present review,we discussed the molecular mechanism of MALAT1 and summarized the current knowledge of its expression in ***,we highlighted the potential use of MALAT1 as a biomarker,including liquid biopsy.

关键词： Long noncoding RNA Gastric carcinogenesis Transcriptional levels Posttranscriptional levels Prognostic biomarker Liquid biopsy

Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2276-2289页

作者： Oscar Gonzalez‑Recio Adrian Lopez‑Catalina Ramon Peiro‑Pastor Alicia Nieto‑Valle Monica Castro Almudena Fernandez Dpt.Mejora genetica Animal INIA-CSICCtra La Coruna Km 7.528040 MadridSpain. ETSIAAB Universidad Politecnica de Madrid.Ciudad Universitaria S/N28040 MadridSpain.

Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the *** requires a low sequencing depth to be cost effective,which may increase the error at the genotype *** generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to *** aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks *** Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank *** LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)*** This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high *** may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is *** addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

关键词： Genomic selection Genomic values Low pass sequencing Low sequencing imputation Polygenic risk score

Can sexual selection and disassortative mating contribute to the maintenance of a shell color polymorphism in an inter- tidal marine snail？

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Current Zoology 2012年第3期58卷 463-474页

作者： Emilio ROLALVAREZ Maria SAURA Angel E DIZ Marfa JOSE RIVAS MargaALVAREZ Beatriz CORTES Alicia de COO Daniel ESTEVEZ Laura IGLESIAS Departamento de Bioqufmica Genetica e Inmunologfa Facultad de Biologfa Universidad de Vigo Campus de Vigo 36310 VigoSpain

Littorina fabalisis an intertidal snail commonly living on the brown algaeFucus vesiculosusand showing frequent shell-color polymorphisms in the wild. The evolutionary mechanism underlying this polymorphism is currently unknown. Shell color variation was studied in mated and non-mated specimens of this species from different microareas in one locality from NW Spain, in order to estimate sexual selection and assortative mating that may (still) be operating in this population. The analyses across microareas allowed us to investigate frequency-dependent selection and assortative mating components, mechanisms that could maintain the polymorphism. The presence of shell scars caused by crab attacks, an environmental variable not related with sexual selection or assortative mating, was used as experimental control. This study provides new evidence of significant disas-sortative mating and some degree of sexual selection against some shell colors, supporting the results found 21 years ago in a similar study, i.e. in the same species and locality. The similarity of these estimates during the studied period suggests that this experimental approach is consistent and valid to be extended to other populations and organisms. In addition, sexual selection and assortative mating estimates did not change across microareas differing in shell color frequencies, suggesting than the polymorphism can not be maintained by a frequency-dependent (sexual selection-based) mechanism. Our main hypothesis is that negative assortative mating could contribute to the maintenance of the polymorphism, perhaps by males showing distinct female color preferences when searching for mates.

关键词：多态性潮间带交配壳色蜗牛频率依赖性海洋颜色变化

A catalog of gliadin alleles:Polymorphism of 20th-century common wheat germplasm

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The Crop Journal 2018年第6期6卷 628-641页

作者： Eugene Metakovsky Viktor Melnik Marta Rodriguez-Quijano Vladimir Upelniek Jose Maria Carrillo Unidad de genetica Universidad Politecnica de MadridMadridSpain Vavilov Institute of General Genetics Russian Academy of Sciences MoscowRussia

A new, improved version of the catalog of 182 alleles at the six Gli loci of common wheat(*** L.) shown in electrophoregrams of 128 standard genotypes was used for analysis of1060 cultivars and lines bred in the 20 th century. The most frequent alleles in the studied germplasm occurred with frequencies of 18%–40%, with 30 unique alleles, one in each cultivar. Extremely high genetic diversity was found(average H for the six main Gli loci was0.870 ± 0.046), nearly identical in winter(H = 0.831) and spring(H = 0.856) wheats but differing among 28 groups of cultivars released in 22 countries. Each country or region was characterized by its own specific set of the most frequent Gli alleles, and the 28 cultivar groups formed five main relationship clusters if polymorphism at the six Gli loci was considered. However, different levels of similarity between groups of cultivars were found if polymorphism of the A, B, or D genomes of common wheat was tested separately. In general, the 20 th century germplasm of common wheat was differentiated and structured by country or region and cultivar type(spring or winter). Each elemental genome(in particular, A and D) contributed to the structure of the polymorphism studied. We propose that the structure of the wheat germplasm was a result of natural selection under the ecoclimatic conditions of cultivation specific to each country or region. As many as 27.4% of cultivars studied violated the requirement of the DUS rules for uniformity, being represented by mixtures of two or more closely related genotypes. However, the composition of a cultivar as a set of related but different genotypes may contribute to its adaptivity, and thereby to the known high plasticity of common wheat.

关键词： Gliadin alleles Genetic variation Gene geography Intra-varietal non-uniformity Allopolyploid Triticum aestivum

Dose escalation of adalimumab as a strategy to overcome anti-drug antibodies:A case report of infantile-onset inflammatory bowel disease

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World Journal of Gastroenterology 2023年第38期29卷 5428-5434页

作者： Silvana Ancona Sara Signa Chiara Longo Giuliana Cangemi Roberta Carfora Enrico Drago Alessandro La Rosa Marco Crocco Andrea Chiaro Paolo Gandullia Serena Arrigo Dipartimento di Neuroscienze RiabilitazioneOftalmologiaGenetica e Scienze Materno-Infantili(DINOGMI)Universitàdegli Studi di GenovaGenova 16126Italy Pediatric Gastroenterology and Endoscopy Unit IRCCS Istituto Giannina GasliniGenova 16147Italy Chromatography and Mass Spectrometry Section Central Laboratory of AnalysisIRCCS Istituto Giannina GasliniGenova 16147Italy

BACKGROUND Treatment of infantile-onset inflammatory bowel disease(IO-IBD)is often challenging due to its aggressive disease course and failure of standard therapies with a need for *** loss of response is frequently caused by the production of anti-drug antibodies,a well-known problem in IBD patients on biologic *** present a case of IO-IBD treated with therapeutic drug monitoring(TDM)-guided high-dose anti-tumor necrosis factor therapy,in which dose escalation monitoring was used as a strategy to overcome anti-drug *** SUMMARY A 5-mo-old boy presented with a history of persistent hematochezia from the 10th d of life,as well as relapsing perianal abscess and growth ***,anemia,and elevated inflammatory markers were also *** assessment revealed skip lesions with deep colic ulcerations,inflammatory anal sub-stenosis,and deep fissures with persistent abscess.A diagnosis of IO-IBD Crohn-like was *** patient was initially treated with oral steroids and *** the perianal abscess healed,adalimumab(ADA)was administered with concomitant gradual tapering of *** and biochemical steroid-free remission was achieved with good trough *** 3 mo,antibodies to ADA(ATA)were found with undetectable trough levels;therefore,we optimized the therapy schedule,first administering 10 mg weekly and subsequently up to 20 mg weekly(2.8 mg/kg/dose).After 2 mo of high-dose treatment,ATA disappeared,with concomitant high trough levels and stable clinical and biochemical remission of the *** TDM-guided high-dose ADA treatment as a monotherapy overcame ATA *** strategy could be a good alternative to combination therapy,especially in very young patients.

关键词： Infantile-onset inflammatory bowel disease Adalimumab Loss of response Dose escalation Anti-drug antibodies Case report

Identification of Nodulation Genes (nod Locus 5) From Azorhizobium caulinoaans ORS571

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Science China Chemistry 1993年第10期36卷 1177-1185页

作者：高盟生尤崇杓 K.Goethals M.Holsters Department of Biotechnology IAAE Chinese Academy of Agricultural Sciences Beijing 100094 PRC Laboratrium vor genetica Universiteit Gent. B-9000 Gent Belgium

An 800 bp AccI-PUCII DNA containing promoter region of nodABC （Pi）from A. caulinodans ORS571 was cloned and used as a hybridization probe against the chrom（?）some DNA, which led to the identification of another 8.4-kb EcoRI fragment showing homology to P1. A corresponding clone of 8.4-kb DNA was isolated from a pLAFI gene bank （pRG90）. The restriction enzyme analysis and DNA-DNA hybridization of 8.4-kbDNA indicated the P1 homology was located in the 450-bp SmaI-SphI region （P2 region）. Ω insertion deletion of 8.4 kb DNA resulted in a mutant strain ORS571-5 that delayed to nodulate the stems of S. rostrata. This phenotype was complemented by the introduction of pRK84 carrying nod locus 5 DNA.

关键词： nod gene promoter DNA-DNA hybridization Ω factor.

Interactome Analysis of Microtubule-targeting Agents Reveals Cytotoxicity Bases in Normal Cells

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Genomics, Proteomics & Bioinformatics 2017年第6期15卷 352-360页

作者： Andres Julian Gutierrez-Escobar Gina Mendez-Callejas Grupo de Investigaciones Biomedicas y genetica Aplicada-GIBGA Universidad de Ciencias Aplicadas y Ambientales U.D.C.A.Bogota 111166Colombia

Cancer causes millions of deaths annually and microtubule-targeting agents （MTAs） are the most commonly-used anti-cancer drugs. However, the high toxicity of MTAs on normal cells raises great concern. Due to the non-selectivity of MTA targets, we analyzed the interaction net- work in a non-cancerous human cell. Subnetworks of fourteen MTAs were reconstructed and the merged network was compared against a randomized network to evaluate the functional rich- ness. We found that 71.4% of the MTA interactome nodes are shared, which affects cellular pro- cesses such as apoptosis, cell differentiation, cell cycle control, stress response, and regulation of energy metabolism. Additionally, possible secondary targets were identified as client proteins of interphase microtubules. MTAs affect apoptosis signaling pathways by interacting with client pro- teins of interphase microtubules, suggesting that their primary targets are non-tumor cells. The paclitaxel and doxorubicin networks share essential topological axes, suggesting synergistic effects. This may explain the exacerbated toxicity observed when paclitaxel and doxorubicin are used in combination for cancer treatment.

关键词： Cancer treatment Microtubule-targeting agentInteractome analysis Cancer biology Apoptosis