bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable light environments induce plastic spectral tuning by regional opsin coexpression in the African cichlid fish, Metriaclima zebra
Authors: Dalton Brian E. , Lu Jessica , Leips Jeff , Cronin Thomas W. , Carleton Karen L. 
Published: July 2015

AbstractCritical behaviours such as predation and mate choice often depend on vision. Visual systems are sensitive to the spectrum of light in their environment, which can vary extensively both within and among habitats. Evolutionary changes in spectral sensitivity contribute to divergence and speciation. Spectral sensitivity of the retina is primarily determined by visual pigments, which are opsin proteins bound to a chromophore. We recently discovered that photoreceptors in different regions of the retina, which view objects against distinct environmental backgrounds, coexpress different pairs of opsins in an African cichlid fish, Metriaclima zebra. This coexpression tunes the sensitivity of the retinal regions to the corresponding backgrounds and may aid in detection of dark objects, such as predators. Although intraretinal regionalization of spectral sensitivity in many animals correlates with their light environments, it is unknown whether variation in the light environment induces developmentally plastic alterations of intraretinal sensitivity regions. Here, we demonstrate with fluorescent in situ hybridization and qPCR that the spectrum and angle of environmental light both influence the development of spectral sensitivity regions by altering the distribution and level of opsins across the retina. Normally, M. zebra coexpresses LWS opsin with RH2Aα opsin in double cones of the ventral but not the dorsal retina. However, when illuminated from below throughout development, adult M. zebra coexpressed LWS and RH2Aα in double cones both dorsally and ventrally. Thus, environmental background spectra alter the spectral sensitivity pattern that develops across the retina, potentially influencing behaviours and related evolutionary processes such as courtship and speciation.
Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation
Authors: Campagna Leonardo , Gronau Ilan , Silveira Luís Fábio , Siepel Adam , Lovette Irby J. 
Published: July 2015

AbstractRecently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced‐representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.
Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fishHerichtys minckleyi
Authors: Magalhaes Isabel S. , Ornelas‐Garcıa Claudia Patricia , Leal‐Cardin Mariana , Ramírez Tania , Barluenga Marta 
Published: July 2015

AbstractUnderstanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The ‘desert cichlid’Herichtys minckleyiis a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco‐morphotypes coexist in small spring‐fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrialDNAand 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister speciesHerichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco‐morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco‐morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages.
The molecular evolution of spiggin nesting glue in sticklebacks
Authors: Seear P. J. , Rosato E. , Goodall‐Copestake W. P. , Barber I. 
Published: July 2015

AbstractGene duplication and subsequent divergence can lead to the evolution of new functions and lineage‐specific traits. In sticklebacks, the successive duplication of a mucin gene (MUC19) into a tandemly arrayed, multigene family has enabled the production of copious amounts of ‘spiggin’, a secreted adhesive protein essential for nest construction. Here, we examine divergence between spiggin genes among three‐spined sticklebacks (Gasterosteus aculeatus) from ancestral marine and derived freshwater populations, and propose underpinning gene duplication mechanisms. Sanger sequencing revealed substantial diversity among spiggin transcripts, including alternatively spliced variants and interchromosomal spiggin chimeric genes. Comparative analysis of the sequenced transcripts and all other spiggin genes in the public domain support the presence of three main spiggin lineages (spiggin A,spiggin Bandspiggin C) with further subdivisions withinspiggin B(B1,B2) andspiggin C(C1,C2).Spiggin Ahad diverged least from the ancestralMUC19, while thespiggin Cduplicates had diversified most substantially. In silico translations of the spiggin gene open reading frames predicted that spiggins A and B are secreted as long mucin‐like polymers, while spiggins C1 and C2 are secreted as short monomers, with putative antimicrobial properties. We propose that diversification of duplicated spiggin genes has facilitated local adaptation of spiggin to a range of aquatic habitats.
Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community
Authors: Garcia Sarahi L. , Buck Moritz , McMahon Katherine D. , Grossart Hans‐Peter , Eiler Alexander , Warnecke Falk 
Published: July 2015

AbstractMicroorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet‐uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high‐quality metagenome‐assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin‐ and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage‐based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to ‘social’ interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring ‘interactomes’ and to overcome our inability to isolate and grow the microbes dominating in nature.
A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Authors: Saita Emilio , Abriata Luciano A. , Tsai Yi Ting , Trajtenberg Felipe , Lemmin Thomas , Buschiazzo Alejandro , Dal Peraro Matteo , de Mendoza Diego , Albanesi Daniela 
Published: July 2015

SummaryThe thermosensor histidine kinase DesK from Bacillus subtilis senses changes in membrane fluidity initiating an adaptive response. Structural changes in DesK have been implicated in transmembrane signaling, but direct evidence is still lacking. On the basis of structure‐guided mutagenesis, we now propose a mechanism of DesK‐mediated signal sensing and transduction. The data indicate that stabilization/destabilization of a 2‐helix coiled coil, which connects the transmembrane sensory domain of DesK to its cytosolic catalytic region, is crucial to control its signaling state. Computational modeling and simulations reveal couplings between protein, water and membrane mechanics. We propose that membrane thickening is the main driving force for signal sensing and that it acts by inducing helix stretching and rotation prompting an asymmetric kinase‐competent state. Overall, the known structural changes of the sensor kinase, as well as further dynamic rearrangements that we now predict, consistently link structure determinants to activity modulation.
A LysR‐family transcriptional regulator required for virulence in Brucella abortus is highly conserved among the α‐proteobacteria
Authors: Sheehan Lauren M. , Budnick James A. , Blanchard Catlyn , Dunman Paul M. , Caswell Clayton C. 
Published: July 2015

SummarySmall RNAs are principal elements of bacterial gene regulation and physiology. Two small RNAs in Brucella abortus, AbcR1 and AbcR2, are required for wild‐type virulence. Examination of the abcR loci revealed the presence of a gene encoding a LysR‐type transcriptional regulator flanking abcR2 on chromosome 1. Deletion of this lysR gene (bab1_1517) resulted in the complete loss of abcR2 expression while no difference in abcR1 expression was observed. The B. abortus bab1_1517 mutant strain was significantly attenuated in macrophages and mice, and bab1_1517 was subsequently named vtlR for virulence‐associated transcriptional LysR‐family regulator. Microarray analysis revealed three additional genes encoding small hypothetical proteins also under the control of VtlR. Electrophoretic mobility shift assays demonstrated that VtlR binds directly to the promoter regions of abcR2 and the three hypothetical protein‐encoding genes, and DNase I footprint analysis identified the specific nucleotide sequence in these promoters that VtlR binds to and drives gene expression. Strikingly, orthologs of VtlR are encoded in a wide range of host‐associated α‐proteobacteria, and it is likely that the VtlR genetic system represents a common regulatory circuit critical for host–bacterium interactions.
Vibrio cholerae phosphatases required for the utilization of nucleotides and extracellular DNA as phosphate sources
Authors: McDonough EmilyKate , Kamp Heather , Camilli Andrew 
Published: July 2015

SummaryPhosphate is essential for life, being used in many core processes such as signal transduction and synthesis of nucleic acids. The waterborne agent of cholera, Vibrio cholerae, encounters phosphate limitation in both the aquatic environment and human intestinal tract. This bacterium can utilize extracellular DNA (eDNA) as a phosphate source, a phenotype dependent on secreted endo‐ and exonucleases. However, no transporter of nucleotides has been identified in V. cholerae, suggesting that in order for the organism to utilize the DNA as a phosphate source, it must first separate the phosphate and nucleoside groups before transporting phosphate into the cell. In this study, we investigated the factors required for assimilation of phosphate from eDNA. We identified PhoX, and the previously unknown proteins UshA and CpdB as the major phosphatases that allow phosphate acquisition from eDNA and nucleotides. We demonstrated separable but partially overlapping roles for the three phosphatases and showed that the activity of PhoX and CpdB is induced by phosphate limitation. Thus, this study provides mechanistic insight into how V. cholerae can acquire phosphate from extracellular DNA, which is likely to be an important phosphate source in the environment and during infection.
Identification of I‐7 expands the repertoire of genes for resistance to Fusarium wilt in tomato to three resistance gene classes
Authors: Gonzalez‐Cendales Yvonne , Catanzariti Ann‐Maree , Baker Barbara , Mcgrath Des J. , Jones David A. 
Published: July 2015

SummaryThe tomato I‐3 and I‐7 genes confer resistance to Fusarium oxysporum f. sp. lycopersici (Fol) race 3 and were introgressed into the cultivated tomato, Solanum lycopersicum, from the wild relative Solanum pennellii. I‐3 has been identified previously on chromosome 7 and encodes an S‐receptor‐like kinase, but little is known about I‐7. Molecular markers have been developed for the marker‐assisted breeding of I‐3, but none are available for I‐7. We used an RNA‐seq and single nucleotide polymorphism (SNP) analysis approach to map I‐7 to a small introgression of S. pennellii DNA (c. 210 kb) on chromosome 8, and identified I‐7 as a gene encoding a leucine‐rich repeat receptor‐like protein (LRR‐RLP), thereby expanding the repertoire of resistance protein classes conferring resistance to Fol. Using an eds1 mutant of tomato, we showed that I‐7, like many other LRR‐RLPs conferring pathogen resistance in tomato, is EDS1 (Enhanced Disease Susceptibility 1) dependent. Using transgenic tomato plants carrying only the I‐7 gene for Fol resistance, we found that I‐7 also confers resistance to Fol races 1 and 2. Given that Fol race 1 carries Avr1, resistance to Fol race 1 indicates that I‐7‐mediated resistance, unlike I‐2‐ or I‐3‐mediated resistance, is not suppressed by Avr1. This suggests that Avr1 is not a general suppressor of Fol resistance in tomato, leading us to hypothesize that Avr1 may be acting against an EDS1‐independent pathway for resistance activation. The identification of I‐7 has allowed us to develop molecular markers for marker‐assisted breeding of both genes currently known to confer Fol race 3 resistance (I‐3 and I‐7). Given that I‐7‐mediated resistance is not suppressed by Avr1, I‐7 may be a useful addition to I‐3 in the tomato breeder's toolbox.
Rotation of male genitalia in various species of phlebotomine sandfly
Authors: VOTÝPKA J. , PAVLASOVA M. , VOLFOVA V. , VOLF P. 
Published: July 2015

AbstractPhlebotomine sandflies, vectors of Leishmania (Kinetoplastida: Trypanosomatidae) parasites that affect millions of people worldwide, breed in terrestrial biotopes. As immature stages are rarely accessible, the detection of their natural breeding sites is primarily based on findings of juvenile males with unrotated external genitalia. In males, permanent 180° rotation on the longitudinal body axis occurs soon after eclosion; however, no study has as yet addressed this aspect in detail. The present study describes the timing and duration of the rotation of male external genitalia in eight highly medically important sandfly species belonging to the genera Sergentomyia, Lutzomyia and Phlebotomus (all: Diptera: Psychodidae), kept under controlled laboratory conditions. The average duration of rotation was species‐specific and varied from 12 h in Sergentomyia schwetzi to 33 h in Phlebotomus sergenti. Significant differences in rotation times were found among species, even between two closely related species of the subgenus Larroussius, Phlebotomus orientalis and Phlebotomus tobbi. The rotation of genitalia in all three studied genera was randomly oriented and similar numbers of clockwise and counter‐clockwise events were observed. The study also addresses the effects of some external factors. In all species studied, rotation was not affected by the time of day of eclosion. Similarly, no differences in total rotation time were found between Phlebotomus papatasi males maintained at 25 and 20 °C, respectively. The present findings will assist in the search for natural breeding sites and in studies aimed at elucidating strategies for integrated sandfly and leishmaniasis control.
Wiring a plant: genetic networks for phloem formation in Arabidopsis thaliana roots
Authors: Rodriguez‐Villalon Antia 
Published: July 2015

SummaryIn plants, phloem conduits form a specialized vascular network mediating the exchange of nutrients and signaling molecules between distantly separated organs. To become effective transport elements, protophloem cells undergo a rather unique, differentiation program that involves nucleus degradation, organelle rearrangement and cell wall thickening. Yet, protophloem sieve elements remain alive because their essential metabolic functions are supported by their neighboring companion cells. In spite of the importance of the phloem, the molecular mechanisms orchestrating protophloem specification and differentiation remain still poorly understood. In this review, I provide a summary of recent discoveries regarding morphogenetic events that determine phloem formation, and also a discussion of the systemic effects on root architecture derived from impaired protophloem differentiation programs.

Contents

Summary
45

I.
Introduction
45

II.
Root phloem formation in Arabidopsis thaliana
46

III.
Genetic regulatory networks controlling phloem specification
46

IV.
Molecular mechanisms regulating phloem differentiation
47

V.
Systemic effects of protophloem differentiation in root architecture
48

VI.
Future perspectives
48

Acknowledgements
49

References
49
Standards for plant synthetic biology: a common syntax for exchange of DNA parts
Authors: Patron Nicola J. , Orzaez Diego , Marillonnet Sylvestre , Warzecha Heribert , Matthewman Colette , Youles Mark , Raitskin Oleg , Leveau Aymeric , Farré Gemma , Rogers Christian , Smith Alison , Hibberd Julian , Webb Alex A. R. , Locke James , Schornack Sebastian , Ajioka Jim , Baulcombe David C. , Zipfel Cyril , Kamoun Sophien , Jones Jonathan D. G. , Kuhn Hannah , Robatzek Silke , Van Esse H. Peter , Sanders Dale , Oldroyd Giles , Martin Cathie , Field Rob , O'Connor Sarah , Fox Samantha , Wulff Brande , Miller Ben , Breakspear Andy , Radhakrishnan Guru , Delaux Pierre‐Marc , Loqué Dominique , Granell Antonio , Tissier Alain , Shih Patrick , Brutnell Thomas P. , Quick W. Paul , Rischer Heiko , Fraser Paul D. , Aharoni Asaph , Raines Christine , South Paul F. , Ané Jean‐Michel , Hamberger Björn R. , Langdale Jane , Stougaard Jens , Bouwmeester Harro , Udvardi Michael , Murray James A. H. , Ntoukakis Vardis , Schäfer Patrick , Denby Katherine , Edwards Keith J. , Osbourn Anne , Haseloff Jim 
Published: July 2015

SummaryInventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease‐mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.
A community genetics perspective: opportunities for the coming decade
Authors: Crutsinger Gregory M. 
Published: July 2015

SummaryCommunity genetics was originally proposed as a novel approach to identifying links between genes and ecosystems, and merging ecological and evolutional perspectives. The dozen years since the birth of community genetics have seen many empirical studies and common garden experiments, as well as the rise of eco‐evolutionary dynamics research and a general shift in ecology to incorporate intraspecific variation. So what have we learned from community genetics? Can individual genes affect entire ecosystems? Are there interesting questions left to be answered, or has community genetics run its course? This perspective makes a series of key points about the general patterns that have emerged and calls attention to gaps in our understanding to be addressed in the coming years.

Contents

Summary
65

I.
Introduction
65

II.
Plant genotype effects are common, especially on herbivores
66

III.
From prey to predators, genetic effects cascade up the food chain
66

IV.
Genetic effects rain down from the canopy to soil
66

V.
The dampening of the extended phenotype
66

VI.
From genetic to species, diversity begets diversity
67

VII.
It's the traits that matter … but which ones?
68

VIII.
There are many, many genes for ecosystems
68

IX.
From the community‐genetic caterpillar to the eco‐evolutionary butterfly
68

X.
Conclusions and future directions
68

Acknowledgements
69

References
69
Toluidine blue aids in detection of dysplasia and carcinoma in suspicious oral lesions
Authors: Chainani‐Wu N , Madden E , Cox D , Sroussi H , Epstein J , Silverman S 
Published: July 2015

ObjectivesAccurate clinical identification of ‘higher‐risk’ oral premalignant lesions or ‘higher‐risk’ areas within lesions is important. Assessment methods that predict their presence have great utility.Subjects and MethodsA cross‐sectional, observational study enrolled a consecutive sample of consenting patients diagnosed with oral leukoplakia, erythroleukoplakia, or erythroplakia. Medical history, visual oral examination, ViziLite® examination, toluidine blue staining (TBlue®), and finally a biopsy were completed in a single clinic visit. Seventy‐seven of 100 examined lesions in 43 patients were biopsied. Sensitivity, specificity, and positive and negative predictive values were computed for visual examination, ViziLite®, and TBlue® using biopsy results as the gold standard.ResultsThe sensitivity of TBlue® in detecting high‐risk lesions (carcinoma in situ or carcinoma) was 94 (71–100, P < 0.0003) and specificity 45 (32–58, P < 0.53), while for carcinoma, sensitivity was 100 (54–100, P < 0.032) and specificity 39 (28–52, P < 0.097). The results of ViziLite® testing either by itself or in combination with the information from toluidine blue testing revealed low sensitivity for the detection of high‐risk lesions.ConclusionsClinical examination of leukoplakia, erythroplakia, or erythroleukoplakia lesions combined with toluidine blue staining may aid in the identification of severe dysplasia (carcinoma in situ) or carcinoma. This may help in determining whether, when, and where (the site within a lesion) a biopsy should be taken.