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A simple leaf with compound gene expression: Indeterminate leaves co-express ARP and KNOX genes
No full textGoing Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Understanding epidermal cell fate specification during plant embryogenesis
Get PDFShoot epidermal identity is critical for plant survival, growth, and interaction with
the environment. Epidermal identity is specified during very early embryogenesis,
and maintained in the outermost cells of the plant throughout the entire life cycle. In
this work I aimed to generate a model for the establishment of basal epidermal cell
fate during embryogenesis based on the analysis of both known and novel regulators.
Loss of function of two HD-ZIP IV transcription factors, ATML1 and PDF2 had
previously been shown to lead to embryo lethality due to loss of epidermal
specification. In this study I uncover dosage dependency of ATML1 and PDF2
function during embryogenesis. By expressing functional ATML1 and PDF2 fusion
proteins specifically in the epidermis, I developed a novel tool allowing
demonstration of homo- and heterodimerization of these two transcription factors in
planta. Using genetic and proteomic analysis I provide evidence that other HD-ZIP
IV proteins are involved in epidermal specification together with ATML1 and PDF2,
suggesting the presence of multiple regulatory protein complexes.
Based on previous published and unpublished work, I tested the hypothesis that
ATML1 and PDF2 form part of a regulatory feedback loop necessary for
maintenance of epidermal identity, and involving cell-cell signalling mediated by the
receptor kinase ACR4. Using a genetic approach I confirm that ATML1 and PDF2
likely act together with ACR4 in the specification of embryonic epidermal identity. I
show that ATML1 and PDF2 negatively regulate both ACR4, and their own
expression, most likely by binding to L1 box motifs. In contrast, I provide evidence
that ACR4-mediated signalling participates in maintaining expression levels of
ATML1 and PDF2. Mathematical modelling of the properties of the feedback loop
supported by my results, suggests that it is capable of maintaining a robust epidermal
cell fate, and predicts possible changes in network interactions during the process of
epidermal cell fate specification.
Finally I used a combination of bioinformatics approaches to integrate in silico and
experimental data with the aim of discovering potential novel epidermal regulators
and targets of epidermal fate specifying pathways. This work highlighted potential
roles for WOX-family transcription factors in epidermal fate specification, which
were further analysed genetically. In addition, bioinformatics analysis pinpointed an
intriguing overlap between the targets of epidermal specification pathways and
targets of abiotic stresses signalling
Manipulation of host S-nitrosylation by Pseudomonas syringae
Get PDFNitric oxide (NO) and S-nitrosothiols (SNOs) are widespread signalling molecules that
regulate immunity in animals and plants (Wendehenne et al., 2001). Previously, we have
reported that Arabidopsis thaliana S-nitrosoglutathione reductase, (AtGSNOR1) modulates
the extent of total cellular SNO formation, which subsequently regulates multiple modes of
plant disease resistance (Feechan et al., 2005). Loss-of-function mutations in AtGSNOR1,
leading to increased SNO levels, have recently been shown to result in S-nitrosylation of the
key defence regulators NPR1 and AtSABP3, blunting their activity and subsequently leading
to increased pathogen susceptibility (Tada et al., 2008; Wang et al., 2009). Thus, inhibiting
AtGSNOR1 function leading to increased SNOs, would potentially provide a good strategy
for bacterial effector proteins, delivered by the type III secretion system (TTSS), to promote
infection.
AtGSNOR1 is constitutively expressed in all organs in Arabidopsis and its expression is
induced by wounding stress avirulent and non-host pathogen. Using gas phase
chemiluminescence, we show that infection with Pseudomonas syringae pv. tomato strain
DC3000 (PstDC3000) resulted in increase SNO levels which is TTSS. At the same time,
RT-PCR and GUS analysis indicated that AtGSNOR1 expression was transiently suppressed
by PstDC3000 which is also TTSS-dependent. Therefore, PstDC3000 infection suppresses
denitrosylase function of AtGSNOR1 to increase SNO levels and this virulence effect is
delivered by at least one of the effector protein secreted through TTSS.
Several putative cis-acting elements were identified in AtGSNOR1 promoter through deletion
analysis including GT-box, W-box and MYB/MYC binding motif. These elements comprise
of positive and negative regulators which are critical for the induction and suppression of
AtGSNOR1 in response to pathogen infection.
A few transgenic plants expressing effector proteins were selected and tested for their
suppressive effect on AtGSNOR1 expression during PstDC3000 infection. HopAM1 effector
proteins showed the ability to suppress AtGSNOR1 when expressed in planta
Uncovering the roles of SUMOylation in pathogenesis and plant defence
Get PDFSUMOylation is a post-translational modification in which the small ubiquitinlike
protein SUMO is attached to lysine residues of the target protein. In plants,
wide-spread SUMOylation is observed upon a variety of different stress cues. We
tested Arabidopsis SUMOylation machinery knockout mutants for impaired
disease resistance against Pseudomonas syringae pv. tomato (Pst) and identified
sumo2-1, sae1a-1 and sae2-3 as showing moderate but statistically insignificant
resistance. sumo2-1 also exhibited slightly reduced HR compared to the wild-type
plants after PstDC3000(avrB) challenge. Change in the cellular redox status is an
important outcome of attempted pathogen ingress. Therefore, we also looked at
the redox regulation of SUMOylation both in vivo and in vitro. We found a
significant increase in SUMO1/2 conjugation and free SUMO1/2 accumulation in
atgsnor1-3 plants after PstDC3000(avrB) challenge which was reversed during
the establishment of disease in the absence of an AvrB, suggesting an important
role of S-nitrosylation in modulating plant SUMOylation. High basal level of high
molecular weight (HMW) SUMO1/2 conjugates was also apparent in atgsnor1-3
plants even in the absence of pathogens. The changes in SUMO3 and SUMO5
remained less significant and their regulation was found to be independent of
GSNOR. Biotin switch technique was employed to test further if SUMO enzymes
are modified by NO. It was found that SCE1 and SAE1a are S-nitrosylated in
vitro in a GSNO dose dependent fashion. MS analysis and site directed
mutagenesis revealed Cys139 in SCE, and Cys93, Cys158 and Cys231 in SAE1a as
the targets of S-nitrosylation. We established that GSNO treatment to SCE1
differentially regulates in vitro SUMOylation of the model substrate ScPCNA.
Furthermore, the S-nitrosylation of Cys139 of SCE1 is important in fine-tuning
protein SUMOylation under changing cellular redox tone. These data highlight
the complexity of cross-communication between two different post-translational
modifications (i.e. S-nitrosylation and SUMOylation) in the control of protein
function
Is mutational meltdown a threat to the mega diverse genus Begonia?
Get PDFBegonia is one of the most species-rich angiosperm genera, studied for its rapid
species radiation in tropical regions, and high morphological diversity. Typical
populations are isolated and many display characteristics of narrow endemism.
Endemic populations are prone to inbreeding and vulnerable to anthropogenic
disturbance, while being isolated and difficult to access for population size
estimation. For these rare species, herbarium specimens are the most accessible
material available, even though the number of specimens collected for a single
population is few.
We have developed a pipeline to use genomic data recovered from a single
herbarium specimen to estimate the degree of inbreeding and the demographic
history of the population. This pipeline has been designed to process low-coverage
ancient DNA datasets from non-model organisms and assess the inbreeding
coefficient using several genomic homozygosity estimators.
The pipeline integrate several tools to manage ancient DNA (aDNA) damage
patterns, duplicated genes, problematic baits, and to determine homozygosity
patterns in fresh and historical specimens.
The pipeline includes mapDamage, a tool to quantify nucleotides substitution
A to G or C to T in the set of data, and recalibrate the quality score of the
alignment files, minimizing the bias due to aDNA patterns of damages.
Target capture baits matching multiple regions of the genome have been
identified, characterised, and removed from the analysis as well to prevent
subsequent incorrect variant call.
Many paralogous genes are found in Begonia genomes due to an early whole
genome duplication event in the history of the genus. As this can introduce a bias
in the variant calling step of the pipeline, we have implemented a step to detect
baits capturing sequences from paralogous genes in our analysis. Three methods
have been considered for this: deviation of the genotype frequencies expected
in a mapping population, detection of a unexpected level of heterozygosity
(HDplot tool), or segregating multiple contigs aligning to the same bait (pipeline
HybPiper). This analysis used genome skims from a mapping population to test
the approaches. The study showed low overlap between the baits detected as
capturing paralogs between the three methods with only 73 detected in all of
them.
Herbarium historical specimens from a single population are scarce, and at
one time point considered we can expect to find a reduced number of specimens
available for analysis. In a lot of cases, only a unique specimen is available
and represent the whole population. Therefore, rather than using inbreeding
coefficients based on alleles frequencies, we are using Runs of Homozygosity
(ROH) to estimate inbreeding and need only a single sample to be measured. To
be able to measure ROH with Hyb-Seq data, we needed to know what part of
the genome the Begonia baits are capturing with contiguous baits. The length of
genome captured by the bait set has been calculated for the four most complete
Begonia genomes available to determine the length of syntenic regions which can
be captured.
This was a key point to establish the last part of the pipeline to calculate
the size of ROH. We used PLINK to detect and quantify ROHs from VCF files
produced by variant calling. The estimators derived are the total length of ROH
in the dataset (SROH), the total number of ROH in the dataset (NROH), and
the frequency of ROH for each sample (FROH). The confrontation of the SROH
and NROH scores on a scatter plot provide an estimation of the relative size
of the population, and give clues about an admixture with another population,
a bottleneck event, or consanguinity are provided by this plot. The FROH
estimator is less informative but follows linearly the size of the population
estimated by the NROH/SROH plot. It has been used to study the biogeography
of the specimens and mapped to their phylogenetic reconstruction to investigate
the patterns of homozygosity.
We have analysed two sets of target-capture data with the pipeline, one with
Arabian Begonia, and the second with Begonia from Papua New Guinea.
The first set is composed of 43 specimens of Arabian Begonia specimens from
the Socotran archipelago including the species B. socotrana and B. samhaensis
and with silica-dried and herbarium-dried historical specimens. Examination of
the Hyb-Seq Socotran dataset revealed uneven coverage across the baits. This
capture has been used to show the limitation of the pipeline, as phylogenetic
reconstruction has not been successful beyond species level, and the ROH
estimations were not significant.
The second set of target capture data included 160 samples from the New
Guinea Highlands, from silica-dried and herbarium-dried historical specimens. As
output of the pipeline, 10 specimens showed high homozygosity levels indicating
a bottleneck in their demographic history, 3 outliers were suspected to be inbred,
60 were found to be from a large population or showing introgression, and 87
did not display homozygosity patterns significant enough and were filtered out
by the pipeline. Mapping FROH metrics to the phylogeny shows a group within
section Petermannia with consistently high homozygosity levels. Biogeographical
analysis of the distribution of the samples did not reveal any clear relation between
patterns of homozygosity and geographic location of the populations sampled.
The data analysis has revealed a higher genetic diversity than expected in the
Papua New Guinea Begonia collected and has given clues about the origin of
the homozygosity patterns observed which seem more related to phylogenetic
relationship rather than microevolution at population level
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