Hormonal regulation of fruit set, parthenogenesis induction and fruit expansion in Japanese pear

The effects of applied gibberellins (GAs), GA₁, GA₃, GA₄ and GA₇ with a cytokinin, N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) and indole-3-acetic acid (IAA) on fruit set, parthenogenesis induction and fruit expansion of a number of Rosaceae species were assessed. These included Japanese pear cv. ‘Akibae’ (self-compatible) and cv. ‘Iwate yamanashi’ (a seedless cultivar). Other Rosaceae species (Pyrus communis, Chaenomeles sinensis, Cydonia oblonga, and Malus pumila) were also investigated. GA₄, GA₇ and CPPU are very effective in inducing parthenocarpic fruit growth, whereas GA₁, GA₃ and IAA, have no ability to induce parthenogenesis in Japanese pear. GA₄- and GA₇-induced parthenocarpic fruit tended to be smaller in size, higher in flesh hardness, and showed advanced fruit ripening in comparison to pollinated fruit and to parthenocarpic fruit induced by CPPU. GA₄- and GA₇-induced parthenocarpic fruit also had an increased pedicel length and fruit shape index and also showed a slight protrusion of the calyx end. CPPU, GA₄ and GA₇ alone or combination with uniconazole were also active in inducing parthenogenesis in three other Rosaceae species, although final fruit set was extremely low. GA₁ was essentially inactive in promoting fruit expansion unlike the other bioactive GAs, whose effectiveness in promoting fruit cell expansion was as follow: GA₄ ≈ GA₇ > GA₃ > GA₁.     

Cytoplasmic targeting of mutant poly(A)-binding protein nuclear 1 suppresses protein aggregation and toxicity in oculopharyngeal muscular dystrophy

Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by progressive eyelid drooping, swallowing difficulties and proximal limb weakness. The autosomal dominant form of this disease is caused by a polyalanine expansion from 10 to 12-17 residues, located at the N-terminus of the poly(A)-binding protein nuclear 1 (PABPN1). A distinct pathological hallmark of OPMD is the presence of filamentous intranuclear aggregates in patients' skeletal muscle cells. Wildtype PABPN1 protein is expressed ubiquitously and was shown to be mostly concentrated in discrete nuclear domains called 'speckles'. Using an established cell- culture model, we show that most mutant PABPN1- positive (alanine expanded form) intranuclear aggregates are structures distinct from intranuclear speckles. In contrast, the promyelocytic leukaemia protein, a major component of nuclear bodies, strongly colocalized to intranuclear aggregates of mutant PABPN1. Wildtype PABPN1 can freely shuttle between the nucleus and cytoplasm. We determined whether the nuclear environment is necessary for mutant PABPN1 inclusion formation and cellular toxicity. This was achieved by inactivating the mutant PABPN1 nuclear localization signal and by generating full-length mutant PABPN1 fused to a strong nuclear export sequence. A green fluorescence protein tag inserted at the N-terminus of both wildtype PABPN1 (ala10) and mutant PABPN1 (ala17) proteins allowed us to visualize their subcellular localization. Targeting mutant PABPN1 to the cytoplasm resulted in a significant suppression of both intranuclear aggregates formation and cellular toxicity, two histological consequences of OPMD. Our results indicate that the nuclear localization of mutant PABPN1 is crucial to OPMD pathogenesis.     

Passiflora plastome sequencing reveals widespread genomic rearrangements

Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.     

Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans

A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in‐situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai. Am J Phys Anthropol 150:618–631, 2013. © 2013 Wiley Periodicals, Inc.     

A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

苏北海滨湿地互花米草种子特征及实生苗生长

摘　要　在江苏盐城新洋港滩涂由海向陆建立样地：零星互花米草(Spartina alterniflora)斑块(SAP)?稳定互花米草滩下边缘(SAFI)?2003年互花米草定居处(SAF03)?1989年互花米草定居处(SAF89),对互花米草的种子特征及幼苗生长进行了研究。结果表明：(1) 各样地种子产量有极显著差异(p< 0.01),大小顺序为SAP > SAF03 > SAFI > SAF89,种子产量与植株结实率、穗长、单穗种子数成正比。(2) 4月份SAP、SAFI、SAF03和SAF89互花米草短暂土壤种子库分别为673.7 /m2、2328.7 /m2、5948.8 /m2和3990.4 /m2,种子保存率分别为0.5%、3.9%、6.9%和15.8%,且在各样地差异极显著(p< 0.01)。(3) 7月份SAP、SAFI、SAF03和SAF89实生苗数分别为72 /m2、5 /m2、0和0。SAP与SAFI种子萌发率显著高于SAF03与SAF89(p< 0.01)。(4)表层土壤水分含量和种群内部光照衰减是影响实生苗生长的关键因素。在表层土壤水分含量高和低光照衰减的生境中种子繁殖对互花米草种群延续和扩张贡献较大。     

Inversely density-dependent natal dispersal in brown bears Ursus arctos

There is considerable controversy in the literature about the presence of density dependence in dispersal. In this study, we exploit a data series from a long-term study (>18 years) on radio-marked brown bears (Ursus arctos L.) in two study areas in Scandinavia to investigate how individual-based densities influence the probability of natal dispersal and natal dispersal distances. Cumulatively, 32% and 46% of the females and 81% and 92% of the males dispersed before reaching 5 years of age in the northern and southern study area, respectively. Density had a negative effect on both the probability of dispersal and dispersal distances for the dispersing animals, when controlling for study area, sex and age, making this the first study to show that natal dispersal probability and distances are inversely density dependent in a large carnivore. We suggest that female–female competition for space caused females in higher density areas to settle closer to their natal area. For males, however, merging of demes, resulting in decreased relatedness and increased heterozygosity in an expanding population, might be the reason for shorter dispersal distances in males living at higher densities. This has been hypothesised for small mammals. The high proportion of dispersing female brown bears in Scandinavian compared with North American studies might be due to lower densities in Scandinavia and recent population expansion, with unoccupied areas available at the edges of the population. The longer dispersal distances in female Scandinavian brown bears suggest less social constraints on movements than for North American females. The longer dispersal distances by Scandinavian males may be due to increased searching for potential mates in peripheral areas with lower densities of females. These results, in addition to results of other brown bear studies, suggest that brown bears might be more territorial than previously thought, and that density is regulated by social interactions.     

Condensed,Microtubule-coating Thin Organelles for Orthogonal Translation in Mammalian Cells

Membraneless organelles are capable of selectively performing complex tasks in living cells despite dynamically exchanging with their surroundings. This is an exquisite example how self-organization of proteins and RNAs can lead to more complex functionalities in living systems. Importantly, the absence of a membrane boundary can enable easier access to larger macromolecular complexes that can be challenging to be transported across a membrane. We previously formed orthogonally translating designer membraneless organelles by combining phase separation with kinesin motor proteins to highly enrich engineered translational factors in large organelles. We also showed that even submicron thick designer organelles can be formed, by mounting them onto membranes, which, presumable assisted by 2D condensation, leads to thin film-like condensates. In this study we show that orthogonal translation can also be built with fiber-like appearing organelles. Here, the microtubule-end binding protein EB1 was used to form fiber-like OT organelles along the microtubule cytoskeleton that perform highly selective and efficient orthogonal translation. We also show an improved simplified design of OT organelles. Together this extends OT organelle technology and demonstrates that the microtubule cytoskeleton is a powerful platform for advanced synthetic organelle engineering.     

Limited phylogeographic structure in the flightless ground beetle, Calathus ruficollis, in southern California

The California Floristic Province is home to more than 8000 species of beetles, yet their geographical patterns of supra- and infraspecific diversity remain largely unexplored. In this paper, we investigate the phylogeography and population demographics of a flightless ground beetle, Calathus ruficollis (Coleoptera: Carabidae), in southern California. We sampled 136 specimens from 25 localities divided into 10 populations using a fragment of the mitochondrial cytochrome oxidase I gene. We tested several hypotheses, including the association of geography with particular clades and populations, the degree of differentiation among regions, and the expansion of populations. Parsimony and Bayesian phylogenetic analyses along with nested clade analysis and amova indicate a deep split between the southern Sierra Nevada population and populations south and west. This split corresponds closely to the split between subspecies C. ruficollis ignicollis (southern Sierra Nevada) and C. ruficollis ruficollis . Populations otherwise exhibit limited geographical structure, though F st values indicate some local differentiation. Mismatch distributions and Fu's F s indicate range expansion of several populations, suggesting that some structure may have been obscured by recent exchange. The population of C. ruficollis on Santa Cruz Island, which might have been expected to be isolated, shares several haplotypes with mainland populations, appearing to represent multiple colonizations.     

城市扩张与耕地保护耦合对陆地生态系统碳储量的影响——以湖北省为例

城市扩张对生态系统的影响可以分为城市扩张对生态用地的直接挤占以及为补充城市扩张占用的耕地对生态用地二次挤占两个连锁的过程。以往的研究大多只关注城市扩张对生态系统的直接影响,忽略了城市扩张与耕地保护耦合的间接影响。针对这一问题,采用GIS空间分析方法和InVEST模型定量评估了2000年至2015年湖北省城市扩张与耕地保护耦合对陆地生态系统碳储量的影响。结果显示:(1)城市扩张与耕地保护耦合导致湖北省陆地生态系统碳储量减少40.90 Tg;(2)由城市扩张与耕地保护耦合导致的陆地生态系统碳储量的减少量中,耕地保护传导作用间接导致的占比31%。结果表明,城市扩张与耕地保护的耦合是导致生态系统碳储量减少的主要原因之一。忽视城市扩张通过耕地保护的传导作用对生态系统碳储量的间接影响,会导致城市扩张对陆地生态系统碳储量的影响被严重低估。