Combined hepatocellular cholangiocarcinoma: A clinicopathological update

Combined hepatocellular-cholangiocarcinoma(cHCC-CCA)is a rare primary liver cancer associated with an appalling prognosis.The diagnosis and manage-ment of this entity have been challenging to physicians,radiologists,surgeons,pathologists,and oncologists alike.The diagnostic and prognostic value of biomarkers such as the immunohistochemical expression of nestin,a progenitor cell marker,have been explored recently.With a better understanding of biology and the clinical course of cHCC-CCA,newer treatment modalities like immune checkpoint inhibitors are being tried to improve the survival of patients with this rare disease.In this review,we give an account of the recent developments in the pathology,diagnostic approach,and management of cHCC-CCA.

The complete chloroplast genomic landscape and phylogenetic analyses of Populus alba L.

Populus alba is a foundation species in evolutionary and ecological studies in the northern hemisphere.In this study,the chloroplast genome and gene map of P.alba were constructed.The P.alba chloroplast genome is 156,505 bp in length comprising a large single-copy region,two inverted repeat regions and a small single-copy region.The genome contains 131 genes,including 86 protein-coding genes(77 PCG species),eight ribosomal RNA genes(four rRNA species)and 37 transfer RNA genes(30 tRNA species).Phylogenetic analysis indicates that all Populus chloroplast genome sequences are clustered together and divided into three large branches.Among reported Populus chloroplast genomes,the leuce section formed monophyletic,indicating that all Populus spp.have a common maternal ancestor.P.rotundifolia and P.tremula are closely related and are sisters to P.davidiana.P.alba is closely related to P.adenopoda.Population genetic research in ecology and evolution may be easily developed through chloroplast genomes as they are conserved.This research will benefit future studies related to Populus,one of the world’s most ecologically and economically important genera.

Avian introgression in the genomic era

Introgression,the incorporation of genetic material from one(sub)species into the gene pool of another by means of hybridization and backcrossing,is a common phenomenon in birds and can provide important insights into the speciation process.In the last decade,the toolkit for studying introgression has expanded together with the development of molecular markers.In this review,we explore how genomic data,the most recent step in this methodological progress,impacts different aspects in the study of avian introgression.First,the detection of hybrids and backcrosses has improved dramatically.The most widely used software package is STRUCTURE.Phylogenetic discordance(i.e.different loci resulting in discordant gene trees) is another means for the detection of introgression,although it should be regarded as a starting point for further analyses,not as a definitive proof of introgression.Specifically,disentangling introgression from other biological processes,such as incomplete lineage sorting,remains a challenging endeavour,although new techniques,such as the D-statistic,are being developed.In addition,phylogenetics might require a shift from trees to networks.Second,the study of hybrid zones by means of geographical or genomic cline analysis has led to important insights into the complex interplay between hybridization and speciation.However,because each hybrid zone study is just a single snapshot of a complex and continuously changing interaction,hybrid zones should be studied across different temporal and/or spatial scales.A third powerful tool is the genome scan.The debate on which evolutionary processes underlie the genomic landscape is still ongoing,as is the question whether loci involved in reproductive isolation cluster together in ‘islands of speciation' or whether they are scattered throughout the genome.Exploring genomic landscapes across the avian tree of life will be an exciting field for further research.Finally,the findings from these different methods should be incorporated into specific speciation scenarios,which can consequently be tested using a modelling approach.All in all,this genomic perspective on avian hybridization and speciation will further our understanding in evolution in general.

The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq

Coxsackievirus A16(CVA16) is one of major pathogens of hand, foot and mouth disease(HFMD) in children. Long non-coding RNAs(Inc RNAs) have been implicated in various biological processes,but they have not been associated with CVA16 infection. In this study, we comprehensively characterized the landscape of Inc RNAs of normal and CVA16 infected rhabdomyosarcoma(RD)cells using RNA-Seq to investigate the functional relevance of Inc RNAs. We showed that a total of 760 Inc RNAs were upregulated and 1210 Inc RNAs were downregulated. Out of these dysregulated Inc RNAs, 43.64% were intergenic, 22.31% were sense, 15.89% were intronic, 8.67% were bidirectional, 5.59% were antisense, 3.85% were s RNA host Inc RNAs and 0.05% were enhancer. Six dysregulated Inc RNAs were validated by quantitative PCR assays and the secondary structures of these Inc RNAs were projected. Moreover, we conducted a bioinformatics analysis of an Inc RNAs(ENST00000602478) to elucidate the diversity of modification and functions of Inc RNAs. In summary, the current study compared the dysregulated Inc RNAs profile upon CVA16 challenge and illustrated the intricate relationship between coding and Inc RNAs transcripts. These results may not only provide a complete picture of transcription in CVA16 infected cells but also provide novel molecular targets for treatments of HFMD.

Genetic differentiation of grain, fodder and pod vegetable type cowpeas (Vigna unguiculata L.) identified through single nucleotide polymorphisms from genotyping-by-sequencing

The species Vigna unguiculata L.(Walp),commonly known as cowpea,is a multi-purpose legume that has been selected into three subspecies that are divided into grain,fodder and pod(yardlong bean)types.However,genetic bases for distinctions are not well understood.The purpose of this study was to apply genotyping-by-sequencing(GBS)and current reference genome for V.unguiculata to distinguish three subspecies and identify signatures of divergence.The collection of 130 accessions included 128 cultivated from:1)ssp.cylindrica,fodder type;2)ssp.sesquipedalis,pod vegetable type;and 3)ssp.unguiculata,grain type.Two wilds genotypes from spp.dekindtiana and spp.pubescens,were used to anchor phylogeny.A total of 11,083 highly informative single nucleotide polymorphisms(SNPs)were discovered.Wild accessions showed distinct genetic fingerprints and were separated from cultivated subspecies.Principal component analysis showed closer relationship between ssp.unguiculata and ssp.cylindrica compared to ssp.sesquipedalis.Relative differentiation of cultivated subspecies(with Fixation Index,FST)indicated the existence of discrete signatures of selection.This work clarifies the population structure,phylogeny,and domestication of cultivated cowpeas.Furthermore,significant genetic differences between grain and pod vegetable types can provide valuable information for future breeding in three cowpea groups.