‘Dunbar's number’ deconstructed

A widespread and popular belief posits that humans possess a cognitive capacity that is limited to keeping track of and maintaining stable relationships with approximately 150 people. This influential number, ‘Dunbar''s number’, originates from an extrapolation of a regression line describing the relationship between relative neocortex size and group size in primates. Here, we test if there is statistical support for this idea. Our analyses on complementary datasets using different methods yield wildly different numbers. Bayesian and generalized least-squares phylogenetic methods generate approximations of average group sizes between 69–109 and 16–42, respectively. However, enormous 95% confidence intervals (4–520 and 2–336, respectively) imply that specifying any one number is futile. A cognitive limit on human group size cannot be derived in this manner.     

Putting the ‘bio’ into bioinformatics

Bioinformatic analyses have grown rapidly in sophistication and efficiency to accommodate the vast increase in available data. One of the major challenges has been to incorporate the growing appreciation of the complexity of molecular evolution into new analytical methods. As the reliance on molecular data in biology and medicine increases, we need to be confident that these methods adequately reflect the underlying processes of genome change. This special issue focuses on the way that patterns and processes of molecular evolution are influenced by features of populations of whole organisms, such as selection pressure, population size and life history. The advantage of this approach to molecular evolution is that it views genomic change not simply as a biochemical or stochastic process, but as the result of a complex series of interactions that shape the kinds of genomic changes that can and do happen.     

香菇‘申香1644’的选育报告

香菇‘申香1644’是以传统优质栽培品种‘申香215’为亲本,采用多孢自交育种技术选育的新品种。其菌盖纵切面呈凸形,菌盖直径(6.15±0.38) cm,菌盖厚度(2.27±0.42) cm,菇型圆整,菇质紧实,产量高,生物学转化率95%以上。与亲本相比,‘申香1644’在分子标记和栽培性状上均具有明显差异性,其菌盖为浅黄褐色,颜色较亲本浅;菌龄100-105 d,较亲本缩短5-10 d。‘申香1644’菌丝生长适宜温度为22-26 ℃,原基发育适宜温度为16-22 ℃,可在全国范围内进行代料栽培。     

斑玉蕈‘闽真5号’的选育报告

斑玉蕈‘闽真5号’品种系以‘闽真3号’与‘白玉-01’作为亲本,通过原生质体单核化杂交育种技术选育获得。该品种菌盖白色,呈半球形,表面斑纹少而小。鲜菇蛋白质含量2.1%,氨基酸总量1.43%。示范栽培表明,‘闽真5号’菌丝最适培养温度20-27 ℃,子实体生长发育温度12-17 ℃,袋栽菌包培养周期为110 d,出菇周期为28 d,平均单袋产量635.17 g/袋。该品种具有栽培周期短、产量高、商品性状好等优良性状,适用于袋栽工厂化周年栽培。     

香菇‘豫香2号’的选育报告

‘豫香2号’是从河南省卢氏县伏牛山地区采集的野生香菇子实体,经过多次组织分离和驯化等系统选育而获得的优良品种,适宜河南省中高海拔区域种植。该品种子实体中等,多单生,菌盖圆整、浅褐色,菌柄呈倒圆锥形,产量高,鲜销耐储存。     

黑木耳‘高原云耳3号’的选育报告

‘高原云耳3号’由采自云南保山大平坦山区的一株野生黑木耳,通过驯化栽培、组织分离等多代自然选育获得。子实体大小中等,耳片中间层厚、腹面和背面易分离;呈浅口圆碗状,有光泽,质地柔软,无耳脉。采用小孔栽培,开口10 d左右现芽,出耳温度10-26 ℃。产量高,抗逆性强,是性状较好的一个中早熟中低温型品种。适宜海拔1 000-2 000 m的低纬高原地区规模化栽培。     

Genome sequencing and analysis of two early-flowering cherry (Cerasus × kanzakura) varieties, ‘Kawazu-zakura’ and ‘Atami-zakura’

To gain genetic insights into the early-flowering phenotype of ornamental cherry, also known as sakura, we determined the genome sequences of two early-flowering cherry (Cerasus × kanzakura) varieties, ‘Kawazu-zakura’ and ‘Atami-zakura’. Because the two varieties are interspecific hybrids, likely derived from crosses between Cerasus campanulata (early-flowering species) and Cerasus speciosa, we employed the haplotype-resolved sequence assembly strategy. Genome sequence reads obtained from each variety by single-molecule real-time sequencing (SMRT) were split into two subsets, based on the genome sequence information of the two probable ancestors, and assembled to obtain haplotype-phased genome sequences. The resultant genome assembly of ‘Kawazu-zakura’ spanned 519.8 Mb with 1,544 contigs and an N50 value of 1,220.5 kb, while that of ‘Atami-zakura’ totalled 509.6 Mb with 2,180 contigs and an N50 value of 709.1 kb. A total of 72,702 and 69,528 potential protein-coding genes were predicted in the genome assemblies of ‘Kawazu-zakura’ and ‘Atami-zakura’, respectively. Gene clustering analysis identified 2,634 clusters uniquely presented in the C. campanulata haplotype sequences, which might contribute to its early-flowering phenotype. Genome sequences determined in this study provide fundamental information for elucidating the molecular and genetic mechanisms underlying the early-flowering phenotype of ornamental cherry tree varieties and their relatives.     

暗褐网柄牛肝菌‘YL1701-2’的选育报告

以野生驯化栽培品种HZ14080和野生菌株HZ16009为亲本,经孢子单核菌丝有性杂交选育获得YL1701-2。其菌丝生长适温25-32 ℃,子实体发育适温25-32 ℃。该品种具有菌柄粗壮、菌盖厚且大、菇肉紧实、出菇早、抗逆能力强、生长周期短、出菇整齐、成品率较高和产量高的优势;具有伤后不变或轻微变色、特有土味淡和商品化程度高的特点。既可袋栽也可瓶栽,但以瓶栽为主。目前该菌株已大量用于生产且已获得专利授权。     

Biophysical Reviews ‘Meet the editor series’—Addmore Shonhai

It gives me great pleasure to have the opportunity to introduce myself to the readers of Biophysical Reviews as part of the ‘meet the editors’ series. What follows is a mini-autobiography of my life as it relates to my scientific career and research.

     

Targeted ‘knockdown’ of spliceosome function in mammalian cells

The existence of two sophisticated parallel splicing machineries in multicellular organisms has raised intriguing questions—ranging from their impact on proteome expansion to the evolution of splicing and of metazoan genomes. Exploring roles for the distinct splicing systems in vivo has, however, been restricted by the lack of techniques to selectively inhibit their function in cells. In this study, we show that morpholino oligomers complementary to the branch-site recognition elements of U2 or U12 small nuclear RNA specifically suppress the function of the two splicing systems in mammalian cells. The data provide the first evidence for a role of distinct spliceosomes in pre-mRNA splicing from endogenous mammalian genes and establish a tool to define roles for the different splicing machineries in vivo.     

Improving DNA array data quality by minimising ‘neighbourhood’ effects

Gene expression studies using cDNA arrays require robust and sensitive detection methods. Being extremely sensitive, radioactive detection suffers from the influence of signals positioned in each other’s vicinity, the ‘neighbourhood’ effect. This limits the gene density of arrays and the quality of the results obtained. We have investigated the quantitative influence of different parameters on the ‘neighbourhood’ effect. By using a model experimental system, we could show that the effect is linear and depends only on the intensity of the hybridisation signal. We identified a common factor that can describe the influence of the neighbour spots based on their intensities. This factor is <1%, but it has to be taken into account if a high dynamic range of gene expression is to be detected. We could also derive the factor, although with less precision, from comparison of duplicate spots on arrays of 4565 different clones and replication of the hybridisation experiments. The calculated coefficient applied to our actual experimental results not only revealed previously undetected tissue or cell-specific expression differences, but also increased the dynamic range of detection. It thus provides a relatively simple way of improving DNA array data quality with few experimental modifications.     

Suppression of Ripe Rot on ‘Zesy002’ Kiwifruit with Commercial Agrochemicals

Ripe rot caused by Botryosphaeria dothidea is one of the serious diseases of postharvest kiwifruit. In order to control ripe rot on Actinidia chinensis cultivar ‘Zesy002’, several commercial agrofungicides were selected by an antifungal test on an artificial medium. Furthermore, disease suppression by the selected fungicides was evaluated on the kiwifruit by inoculation with a conidial suspension of B. dothidea. On the artificial media containing boscalid + fludioxonil was shown to be the most effective antifungal activity. However, in the bio-test pyraclostrobin + boscalid and iminoctadine-tris were the most effective agrochemicals on the fruit. On the other hand, the infection structures of B. dothidea on kiwifruit treated with pyraclostrobin + boscalid were observed with a fluorescent microscope. Most of the fungal conidia had not germinated on the kiwifruit treated with the agrochemicals whereas on the untreated fruit the fungal conidia had mostly germinated. Electron microscopy of the fine structures showed morphological changes to the conidia and branch of hyphae on the kiwifruit pre-treated with pyraclostrobin + boscalid, indicating its suppression effect on fungal growth. Based on this observation, it is suggested that ripe rot by B. dothidea may be suppressed through the inhibition of conidial germination on the kiwifruit treated with the agrochemicals.