Journal: International Journal of Biometeorology

Article Title: Dissipation of excess excitation energy of the needle leaves in Pinus trees during cold winters

doi: 10.1007/s00484-016-1182-3

Figure Lengend Snippet: The comparison of chlorophyll fluorescence parameters of needles in Pinus trees between in cold winter and summer

Article Snippet: The plants used in this study were specimens of Pinus koraiensis (height 7.2–8.5 m, diameter at breast height 16.3–18.1 cm, tree age 48 years), Pinus tabulaeformis (height 10.1–11.3 m, diameter at breast height 26.9–29.4 cm, tree age 31 years), and Pinus armandi (height 7.9–9.1 m, diameter at breast height 21.0–23.3 cm, tree age 41 years) growing in the botanic garden of Shenyang Agricultural University, Shenyang city, Liaoning Province, China (41° 82′ N, 123° 56′ E).

Techniques: Comparison, Fluorescence

Journal: G3: Genes|Genomes|Genetics

Article Title: Performance of Seven Tree Breeding Strategies Under Conditions of Inbreeding Depression

doi: 10.1534/g3.115.025767

Figure Lengend Snippet: Estimates of inbreeding depression in relation to the additive genetic standard deviation (µ D /σ A ) for growth traits calculated from literature assuming additive coefficients of variation ( CV A ) of 10% for tree height and diameter and 20% for volume ( Cornelius 1994 )

Article Snippet: Pinus elliottii , 2.4–5.2 , 3.7–9.4 , 3.6–8.2 , Matheson et al. 1995 .

Techniques: Standard Deviation

Journal: Bioinformatics

Article Title: Pinetree: a step-wise gene expression simulator with codon-specific translation rates

doi: 10.1093/bioinformatics/btz203

Figure Lengend Snippet: Design and example output of Pinetree. Pinetree is a generic gene expression simulator that tracks individual RNA polymerases on DNA, and ribosome and RNases on mRNA transcripts. RNases are optional and Pinetree can simulate gene expression with or without transcript degradation. (A) A specialized set of reactions mediates binding and movement of ribosomes, RNA polymerases and RNases. These reactions convert molecules from a species pool into individually modeled ribosomes, polymerases, and RNases. (B) Pinetree tracks individual ribosomes and RNA polymerases on transcripts and DNA, respectively. Lightning bolts represent potential collisions. Ribosomes may begin translation before a full transcript has been synthesized by the RNA polymerases. Likewise, an RNase may begin degrading an RNA transcript before the polymerase has synthesized the full transcript. Together, Pinetree allows the end user to define arbitrary reactions between molecules in the free species pool, while still modeling transcription and translation at the single-molecule level. (C) Simulation of a three-gene plasmid with one gene (proteinY) recoded to use rare codons. No RNases are present in this simulation, so no degradation occurs. Translation of proteinY is slower than that of proteinX and rnapol. (D) Ribosome densities on the transcript of proteinY are higher in the recoded gene than in the wild-type. The recoded gene has lower per-codon translation rates than that of the wild-type

Article Snippet: RNases are optional and Pinetree can simulate gene expression with or without transcript degradation. ( A ) A specialized set of reactions mediates binding and movement of ribosomes, RNA polymerases and RNases.

Techniques: Gene Expression, Binding Assay, Synthesized, Plasmid Preparation

Journal: AoB Plants

Article Title: A novel dendroecological method finds a non-linear relationship between elevation and seasonal growth continuity on an island with trade wind-influenced water availability

doi: 10.1093/aobpla/ply070

Figure Lengend Snippet: (A) Location of the Canary Islands, Spain; (B) location of La Palma in the north-west of the Canary Archipelago; (C) mean monthly climate variations on La Palma derived from gridded climate data ; (D) location of the study sites on the windward slope of La Palma; (E) topography of the north-eastern part of La Palma. The locations of the study sites of Pinus canariensis are marked with ‘+’. Each site includes ≥20 tree cores (two per individual) for cross-validation. Overall sample size is >200 cores.

Article Snippet: Pinus canariensis is a palaeo-endemic pine species (Pinaceae) of the Canary Islands ( Wieser et al. 2016 ) that shows adaptation to a wide range of climatic conditions ( López de Heredia et al. 2014 ).

Techniques: Derivative Assay, Biomarker Discovery

Journal: AoB Plants

Article Title: A novel dendroecological method finds a non-linear relationship between elevation and seasonal growth continuity on an island with trade wind-influenced water availability

doi: 10.1093/aobpla/ply070

Figure Lengend Snippet: Sampling locations from (A) typical high-elevation, (B) mid-elevation and (C) low-elevation population of Pinus canariensis on La Palma.

Article Snippet: Pinus canariensis is a palaeo-endemic pine species (Pinaceae) of the Canary Islands ( Wieser et al. 2016 ) that shows adaptation to a wide range of climatic conditions ( López de Heredia et al. 2014 ).

Techniques: Sampling

Journal: AoB Plants

Article Title: A novel dendroecological method finds a non-linear relationship between elevation and seasonal growth continuity on an island with trade wind-influenced water availability

doi: 10.1093/aobpla/ply070

Figure Lengend Snippet: Tree-ring chronology characteristics of Pinus canariensis across the elevational gradient. ‘ N ’: number of trees used to analyse climate–growth relationships; ‘EPS’: expressed population signal; ‘IC’: overall inter-series correlation representing the average pairwise correlation between tree-ring series off a site. n missing refers to the share of missing rings in all years over all cores of a chronology. The chronologies from 327 to 754 m a.s.l. were removed from subsequent climate–growth analysis due to very low EPS and IC values, which is indicated by italic font.

Article Snippet: Pinus canariensis is a palaeo-endemic pine species (Pinaceae) of the Canary Islands ( Wieser et al. 2016 ) that shows adaptation to a wide range of climatic conditions ( López de Heredia et al. 2014 ).

Techniques:

Journal: AoB Plants

Article Title: A novel dendroecological method finds a non-linear relationship between elevation and seasonal growth continuity on an island with trade wind-influenced water availability

doi: 10.1093/aobpla/ply070

Figure Lengend Snippet: Distinct tree-ring (TR) boundaries versus ADF in wood cores of Pinus canariensis from La Palma. (A) Magnified view on a tree core showing an ADF and a neighbouring distinct TR boundary with abrupt stop of latewood formation. The latewood formation of both ADF and TR has comparable dimensions. The ADF is followed by a clearly recognizable TR boundary and two further tree rings with faint latewood boundaries. (B) Thin section showing the same part of the tree core with (C) a magnified view of cell-size transition within an ADF. Arrows indicate the position of smallest late-wood cells where we finished one ring-width measurement and started the next. Images of thin sections by Loïc Schneider.

Article Snippet: Pinus canariensis is a palaeo-endemic pine species (Pinaceae) of the Canary Islands ( Wieser et al. 2016 ) that shows adaptation to a wide range of climatic conditions ( López de Heredia et al. 2014 ).

Techniques:

Journal: AoB Plants

Article Title: A novel dendroecological method finds a non-linear relationship between elevation and seasonal growth continuity on an island with trade wind-influenced water availability

doi: 10.1093/aobpla/ply070

Figure Lengend Snippet: (A) Indices for temperature seasonality (standard deviation of monthly mean temperature) and precipitation seasonality (coefficient of variation of monthly precipitation sum) along the studied elevational gradient derived from gridded climate data ; (B) index for stem growth continuity (percentage of ADFs in the period 1980–2012, definition see text) ranging from 0 (lowest stem growth continuity between years) to 100 % (highest continuity) calculated for all 20 wood cores of Pinus canariensis per stand along the elevational gradient. The fitted line represents the quasi-binomial GLM (quadratic fit, P < 0.001; pseudo- R 2 = 0.36 on 196 degrees of freedom).

Article Snippet: Pinus canariensis is a palaeo-endemic pine species (Pinaceae) of the Canary Islands ( Wieser et al. 2016 ) that shows adaptation to a wide range of climatic conditions ( López de Heredia et al. 2014 ).

Techniques: Standard Deviation, Derivative Assay

Journal: BMC Biology

Article Title: Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

doi: 10.1186/1741-7007-7-84

Figure Lengend Snippet: Estimated divergence times of poorly resolved nodes

Article Snippet: Pinus albicaulis , AGCT , 869509 , 36 , 54.

Techniques: