Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the behavior of each individual differs due to existing genetic and non-genetic variation within the population. It remains unclear how this individuality is managed to achieve collective behavior. We quantify individuality in bands of clonal Escherichia coli cells that migrate collectively along a channel by following a self-generated gradient of attractant. We discover that despite substantial differences in individual chemotactic abilities, the cells are able to migrate as a coherent group by spontaneously sorting themselves within the moving band. This sorting mechanism ensures that differences between individual chemotactic abilities are compensated by differences in the local steepness of the traveling gradient each individual must navigate, and determines the minimum performance required to travel with the band. By resolving conflicts between individuality and collective migration, this mechanism enables populations to maintain advantageous diversity while on the move.

In natural conditions, culms of developing Moso bamboo, Phyllostachys heterocycla var. pubescens, reach their final height of more than ten meters within a short period of two to four months. To study this phenomenon, bamboo culm material collected from different developmental stages and internodes was analyzed. Histological observations indicated that the development of culm was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. Development, maturation, and aging in different regions of the culm were studied systematically from the basal to the top internode. The four major endogenous hormones, indole acetic acid, gibberellic acid, zeatin riboside, and abscisic acid appeared to strongly influence the cell elongation phase. A total of 258 spots were differentially expressed in culm development. Of these, 213 spots were identified by MALDI-TOF/TOF MS and were involved in many physiological and metabolic processes including carbohydrate metabolism, cell division, cell expansion, protein synthesis, amino acid metabolism and redox homeostasis. These proteins with different expression patterns constructed an ingenious network to regulate the culm development. Developmental stage-specific and internode-specific protein expression patterns were identified. Protein abundance was regulated temporally and to some extent spatially, and the sequential development from base to apex of bamboo culm was implemented by temporal and spatial expression of enzymes. Results indicate that during development energy was mainly derived from sucrose degradation, as photosynthetic capacity was poor. The regulation of anaerobic and aerobic modes of respiration appeared to play an important role in energy generation. This is the first report on proteomic profiling in bamboo and helps in understanding the regulatory processes in developing culms.

Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the behavior of each individual will differ due to existing genetic and non-genetic variation within the population. It remains unclear how this individuality is managed to achieve collective behavior. We quantified individuality in bands of clonal Escherichia coli cells that migrate collectively along a channel by following a self-generated gradient of attractant. We discovered that despite substantial differences in individual chemotactic abilities, the cells are able to migrate as a coherent group by spontaneously sorting themselves within the moving band. This sorting mechanism ensures that differences between individual chemotactic abilities are compensated by differences in the local steepness of the traveling gradient each individual must navigate, and determines the minimum performance required to travel with the band. By resolving conflicts between individuality and collective migration, this mechanism enables populations to maintain advantageous diversity while on the move.

BackgroundAs one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (Phyllostachys heterocycla cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.ResultsOur anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.ConclusionsThis is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.

Fruit ripening is a developmental process regulated by a complex network of endogenous and exogenous cues. Sea buckthorn is an excellent material for fruit ripening studies due to its dramatic ripening process and high contents of nutritional and anti-oxidant compounds in berries. Here, the whole transcriptome of sea buckthorn fruit at three development stages were analysed using multiple high-throughput sequencings. We assembled and annotated 9,008 long non-coding RNAs (lncRNAs) in sea buckthorn fruits, and identified 118 differentially expressed lncRNAs (DE-lncRNAs) and 32 differentially expressed microRNAs in fruit developmental process. In addition, we predicted 1,061 cis-regulated and 782 trans-regulated targets of DE-lncRNAs, and these DE-lncRNAs are specifically enriched in the biosynthesis of ascorbic acid, carotenoids and flavonoids. Moreover, the silencing of two lncRNAs (LNC1 and LNC2) in vivo and expression analysis revealed that LNC1 and LNC2 can act as endogenous target mimics of miR156a and miR828a to reduce SPL9 and induce MYB114 expression, respectively, which lead to increased and decreased anthocyanin content as revealed by high-performance liquid chromatography analysis. Our results present the first global functional analysis of lncRNA in sea buckthorn and provide two essential regulators of anthocyanin biosynthesis, which provides new insights into the regulation of fruit quality.

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As the largest K+ transport gene family, KT/HAK/KUP family plays an important role in plant growth, development, and stress adaptation. However, there is limited information about this family in woody plant species. In this study, with genome-wide in-depth investigation, 31 Poplar KT/HAK/KUP transporter genes including six pairs of tandem duplicated and eight pairs of segmental duplicated paralogs have been identified, suggesting segmental and tandem duplication events contributed to the expansion of this family in Poplar. The combination of phylogenetic, exon structure and splice site, and paragon analysis revealed 11 pairs of Poplar KT/HAK/KUP duplicates. For these 11 pairs, all pairs are subject to purify selection, and asymmetric evolutionary rates have been found to occur in three pairs. This study might provide more insights into the underlying evolution mechanisms of trees acclimating to their natural habitat.

HighlightsWe identified 173 AP2/ERF superfamily genes in Salix arbutifolia.A comparative analysis of AP2/ERF superfamily genes was performed.The phylogenic trees of AP2/ERF superfamily have been constructed.