The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome‐level marine mammal genome assembly based on the data generated by the BGISEQ‐500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.     

九种罕见的人类染色体异常核型报告

ReportonNineRareSpeciesofHumanChromosomalAbnormalKaryotypesHanWeitian;QuOu;YuPing;JiangMiao(LiaoningResearchInstituteofFamilyPlanning,Shenyang110031)自1983年以来,我们对数千例不育及胚胎丢失等生殖异常患者进行细胞遗传学研究,发现大量异常染色体核型,而且异常种类繁多,已报道世界首报人类异常核型25种[1]。最近,在不良妊娠患者中又发现9种异常核型,经湖南医科大学医学细胞遗传学国家培训中心鉴定,为世界首次报道．现报告如下。1病例摘要及核型例1男,30岁,表型及智力正常,其妻子妊娠两次,均在无任何诱因情…     

Interleukin-8 Regulates Endothelial Permeability by Down-regulation of Tight Junction but not Dependent on Integrins Induced Focal Adhesions

Interleukin-8 (IL-8) is a common inflammatory factor, which involves in various non-specific pathological processes of inflammation. It has been found that increased endothelial permeability accompanied with high expression of IL-8 at site of injured endothelium and atherosclerotic plaque at early stages, suggesting that IL-8 participated in regulating endothelial permeability in the developing processes of vascular disease. The purpose of this study is to investigate the regulation effects of IL-8 on the vascular endothelial permeability, and the mRNA and protein expression of tight junction components (i.e., ZO-1, Claudin-5 and Occludin). Endothelial cells were stimulated by IL-8 with the dose of 50, 100 and 200 ng/mL, and duration of 2, 4, 6, 8h, respectively. The mRNA and protein expression level of tight junction components with IL-8 under different concentration and duration was examined by RT-PCR and Western blot, respectively. Meanwhile, the integrins induced focal adhesions event with IL-8 stimulation was also investigated. The results showed that IL-8 regulated the permeability of endothelium by down-regulation of tight junction in a dose- and time-dependence manner, but was not by integrins induced focal adhesions. This finding reveals the molecular mechanism in the increase of endothelial cell permeability induced by IL-8, which is expected to provide a new idea as a therapeutic target in vascular diseases.     

Tissue Culture-Induced Heritable Genomic Variation in Rice,and Their Phenotypic Implications

Background

Somaclonal variation generally occurs in plants regenerated from tissue culture. However, fundamental issues regarding molecular characteristics, mutation rates and mutation spectra of plant somatic variation as well as their phenotypic relevance have been addressed only recently. Moreover, these studies have reported highly discrepant results in different plant species and even in the same plant genotype.

Methodology/principal findings

We investigated heritable genomic variation induced by tissue culture in rice by whole genome re-sequencing of an extensively selfed somaclonal line (TC-reg-2008) and its wild type (WT) donor (cv. Hitomebore). We computed the overall mutation rate, single nucleotide polymorphisms (SNPs), small scale insertions/deletions (Indels) and mobilization of transposable elements (TEs). We assessed chromosomal distribution of the various types of genomic variations, tested correlations between SNPs and Indels, and examined concomitancy between TE activity and its cytosine methylation states. We also performed gene ontology (GO) analysis of genes containing nonsynonymous mutations and large-effect mutations, and assayed effects of the genomic variations on phenotypes under both normal growing condition and several abiotic stresses. We found that heritable somaclonal genomic variation occurred extensively in rice. The genomic variations distributed non-randomly across each of the 12 rice chromosomes, and affected a large number of functional genes. The phenotypic penetrance of the genomic variations was condition-dependent.

Conclusions/significance

Tissue culture is a potent means to generate heritable genetic variations in rice, which bear distinct difference at least in space (chromosomal distribution) from those occurred under natural settings. Our findings have provided new information regarding the mutation rate and spectrum as well as chromosomal distribution pattern of somaclonal variation in rice. Our data also suggest that rice possesses a strong capacity to canalize genetic variations under normal growing conditions to maintain phenotypic robustness, which however can be released by certain abiotic stresses to generate variable phenotypes.     

Using embryonic stem cells to form a biological pacemaker via tissue engineering technology

Biological pacemakers can be achieved by various gene‐based and cell‐based approaches. Embryonic stem cells (ESCs)‐derived pacemaker cells might be the most promising way to form biological pacemakers, but there are challenges as to how to control the differentiation of ESCs and to overcome the neoplasia, proarrhythmia, or immunogenicity resulting from the use of ESCs. As a potential approach to solve these difficult problems, tissue‐engineering techniques may provide a precise control on the different cell components of multicellular aggregates and the forming of a construct with‐defined architectures and functional properties. The combined interactions between ESC‐derived pacemaker cells, supporting cells, and matrices may completely reproduce pacemaker properties and result in a steady functional unit to induce rhythmic electrical and contractile activities. As ESCs have a high capability for self‐renewal, proliferation, and potential differentiation, we hypothesize that ESCs can be used as a source of pacemaker cells for tissue‐engineering applications and the ambitious goal of biological cardiac pacemakers may ultimately be achieved with ESCs via tissue‐engineering technology.     

Effects of exogenous B supply on growth, B accumulation and distribution of two navel orange cultivars

To investigate the effects of boron (B) on growth, B concentration and distribution of two navel orange cultivars, ‘Newhall’ (Citrus sinensis Osbeck) and ‘Skagg’s Bonanza’ (Citrus sinensis Osbeck) grafted on the rootstock trifoliate orange [Poncirus trifoliata (L.) Raf.], B at five levels was exogenously supplied to 1-year-old grafted plants of both cultivars under greenhouse conditions. Plants were grown in sand:perlite (1:1, v/v) medium and were irrigated every 2 days with half-strength Hoagland’s No. 2 nutrient solutions containing different B, 0.01, 0.05, 0.10, 0.25 and 2.50 mg l⁻¹ (0.25 and 2.50 mg l⁻¹ were considered as control and excess B treatment, respectively, and the other three B levels were considered as low B treatments). After treatments for 183 days, leaves (from basal, middle, upper parts of the shoots), stem of scion, stem of rootstock and root were separately sampled. Our results showed that plant growth (plant height, root volume and dry weights of various parts) was inhibited in response to low or excess B supplies in both cultivars. It was found that B concentrations in the upper leaves of both cultivars were substantially higher than those in the basal leaves when low concentrations (≤0.05 mg l⁻¹) of exogenous B were applied, suggesting that B was preferentially translocated to the upper-younger leaves to support their growth. Analysis of B distribution in different parts indicated that translocation of B from the root to the scion’s shoots (stems and leaves of scion) may be restricted upon exposure to low B conditions. When B was inadequately supplied, growth of ‘Skagg’s Bonanza’ was better than ‘Newhall’, implying that the former cultivar was more tolerant to low B status, which may be due to the higher efficiency of B translocation from the root to the scion’s shoots. However, when the plants were treated with excess B (2.50 mg l⁻¹), both cultivars showed a similar degree of B toxicity. The probability of scion–rootstock interactions in relation to the differential responses of growth and different efficiency of B translocation involved in the two orange cultivars following the long-term low B stress were discussed.     

Photochemical nature of parietopsin

Parietopsin is a nonvisual green light-sensitive opsin closely related to vertebrate visual opsins and was originally identified in lizard parietal eye photoreceptor cells. To obtain insight into the functional diversity of opsins, we investigated by UV-visible absorption spectroscopy the molecular properties of parietopsin and its mutants exogenously expressed in cultured cells and compared the properties to those of vertebrate and invertebrate visual opsins. Our mutational analysis revealed that the counterion in parietopsin is the glutamic acid (Glu) in the second extracellular loop, corresponding to Glu181 in bovine rhodopsin. This arrangement is characteristic of invertebrate rather than vertebrate visual opsins. The photosensitivity and the molar extinction coefficient of parietopsin were also lower than those of vertebrate visual opsins, features likewise characteristic of invertebrate visual opsins. On the other hand, irradiation of parietopsin yielded meta-I, meta-II, and meta-III intermediates after batho and lumi intermediates, similar to vertebrate visual opsins. The pH-dependent equilibrium profile between meta-I and meta-II intermediates was, however, similar to that between acid and alkaline metarhodopsins in invertebrate visual opsins. Thus, parietopsin behaves as an "evolutionary intermediate" between invertebrate and vertebrate visual opsins.     

Thecate stem medusozoans (Cnidaria) from the early Cambrian Chengjiang biota

Cnidarians are phylogenetically located near the base of the ‘tree of animals’, and their early evolution had a profound impact on the rise of bilaterians. However, the early diversity and phylogeny of this ‘lowly’ metazoan clade has hitherto been enigmatic. Fortunately, cnidarian fossils from the early Cambrian could provide key insights into their evolutionary history. Here, based on a scrutiny of the purported hyolith Burithes yunnanensis Hou et al. from the early Cambrian Chengjiang biota in South China, we reveal that this species shows characters distinct from those typical of hyoliths, not least a funnel-shaped gastrovascular system with a single opening, a whorl of tentacles surrounding the mouth, and the lack of an operculum. These characters suggest a great deviation from the original definition of the genus Burithes, and a closer affinity with cnidarians. We therefore reassign the material to a new genus: Palaeoconotuba. Bayesian inference of phylogeny based on new anatomical traits identifies a new clade, including Palaeoconotuba and Cambrorhytium, as a stem group of sessile medusozoan cnidarians that are united by the synapomorphies of developing an organic conical theca and a funnel-like gastrovascular system. This study unveils a stem lineage of medusozoans that evolved a lifelong conical theca in the early Cambrian.