Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation

2019 ◽  
Vol 366 (11) ◽  
Author(s):  
Gesiele Almeida Barros-Carvalho ◽  
Mariangela Hungria ◽  
Fabrício Martins Lopes ◽  
Marie-Anne Van Sluys
Keyword(s):  
Natural Variation ◽  
Bacterial Genomes ◽  
Phenotypic Differences ◽  
Is Elements ◽  
Local Impact ◽  
Potential Impact ◽  
Symbiotic Properties ◽  
Biological Nitrogen ◽  
Insertional Polymorphism ◽  
Commercial Inoculants

ABSTRACTBradyrhizobium diazoefficiens CPAC 7 and Bradyrhizobium japonicum CPAC 15 are broadly used in commercial inoculants in Brazil, contributing to most of the nitrogen required by the soybean crop. These strains differ in their symbiotic properties: CPAC 7 is more efficient in fixing nitrogen, whereas CPAC 15 is more competitive. Comparative genomics revealed many transposases close to genes associated with symbiosis in the symbiotic island of these strains. Given the importance that insertion sequences (IS) elements have to bacterial genomes, we focused on identifying the local impact of these elements in the genomes of these and other related Bradyrhizobium strains to further understand their phenotypic differences. Analyses were performed using bioinformatics approaches. We found IS elements disrupting and inserted at regulatory regions of genes involved in symbiosis. Further comparative analyses with 21 Bradyrhizobium genomes revealed insertional polymorphism with distinguishing patterns between B. diazoefficiens and B. japonicum lineages. Finally, 13 of these potentially impacted genes are differentially expressed under symbiotic conditions in B. diazoefficiens USDA 110. Thus, IS elements are associated with the diversity of Bradyrhizobium, possibly by providing mechanisms for natural variation of symbiotic effectiveness.

Tsunami-based evidence for large eastern Aleutian slip during the 1957 earthquake

2018 ◽  
Vol 91 (03) ◽  
pp. 1045-1058 ◽  
Author(s):  
Frances R. Griswold ◽  
Breanyn T. MacInnes ◽  
Bretwood Higman
Keyword(s):  
Near Field ◽  
Earthquake Magnitude ◽  
East Central ◽  
Field Surveys ◽  
The Pacific ◽  
Order Of Magnitude ◽  
Local Impact ◽  
Potential Impact ◽  
Run Up ◽  
Eastern Half

AbstractThe Aleutian subduction zone is capable of generating magnitude ~9 earthquakes that have local impact and broadcast their destructive power across the Pacific through tsunamis. Field surveys of the tsunami from the 1957 Great Aleutian earthquake (reported M w 8.6) indicate a tsunami amongst the largest of the twentieth century. In the eastern half of the rupture zone, stranded logs record up to 18 m run-up in the Islands of Four Mountains (IFM) and 32±2 m on Unalaska Island. In conjunction with archaeological studies in the region, these observations show the potential impact of tsunamis on the ancient peoples in the IFM. Simulation of the near-field tsunami produced from the published slip distribution of 1957 is almost an order of magnitude smaller than all field observations. Increasing the earthquake magnitude and amount of eastern slip used in forward models of the tsunami demonstrate that run-up observations can be achieved throughout the eastern Aleutians if the earthquake was more than twice as large—at least M w 8.8 earthquake with 10–20 m of eastern slip. Additionally, up to five possible IFM paleotsunami deposits agree with the regional picture of regular large events, illustrating the circum-Pacific tsunami hazard from the east-central Aleutians.

scholarly journals CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Juan F. Guerra Maldonado ◽  
Antony T. Vincent ◽  
Martin Chenal ◽  
Frederic J. Veyrier
Keyword(s):  
Amino Acid ◽  
Single Species ◽  
Graphical Interface ◽  
Genetic Changes ◽  
Phenotypic Differences ◽  
Phenotypic Divergence ◽  
Potential Impact ◽  
Evolutionary Paths ◽  
User Friendly ◽  
Slow Growing

Abstract Background The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms. Results CAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein’s function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib. Conclusions CAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.

IS elements as constituents of bacterial genomes

1999 ◽  
Vol 150 (9-10) ◽  
pp. 675-687 ◽  
Author(s):  
Jacques Mahillon ◽  
Catherine Léonard ◽  
Michael Chandler
Keyword(s):  
Bacterial Genomes ◽  
Is Elements

Effects of Gender, Parental Role, and Time on Infant- and Adult-Directed Read and Spontaneous Speech

2019 ◽  
Vol 62 (11) ◽  
pp. 4001-4014
Author(s):  
Melanie Weirich ◽  
Adrian Simpson
Keyword(s):  
Parental Involvement ◽  
Gender Identity ◽  
Spontaneous Speech ◽  
First Year ◽  
Space Size ◽  
Vowel Space ◽  
Potential Impact ◽  
Phonetic Features ◽  
And Gender ◽  
Description Task

Purpose The study sets out to investigate inter- and intraspeaker variation in German infant-directed speech (IDS) and considers the potential impact that the factors gender, parental involvement, and speech material (read vs. spontaneous speech) may have. In addition, we analyze data from 3 time points prior to and after the birth of the child to examine potential changes in the features of IDS and, particularly also, of adult-directed speech (ADS). Here, the gender identity of a speaker is considered as an additional factor. Method IDS and ADS data from 34 participants (15 mothers, 19 fathers) is gathered by means of a reading and a picture description task. For IDS, 2 recordings were made when the baby was approximately 6 and 9 months old, respectively. For ADS, an additional recording was made before the baby was born. Phonetic analyses comprise mean fundamental frequency (f0), variation in f0, the 1st 2 formants measured in /i: ɛ a u:/, and the vowel space size. Moreover, social and behavioral data were gathered regarding parental involvement and gender identity. Results German IDS is characterized by an increase in mean f0, a larger variation in f0, vowel- and formant-specific differences, and a larger acoustic vowel space. No effect of gender or parental involvement was found. Also, the phonetic features of IDS were found in both spontaneous and read speech. Regarding ADS, changes in vowel space size in some of the fathers and in mean f0 in mothers were found. Conclusion Phonetic features of German IDS are robust with respect to the factors gender, parental involvement, speech material (read vs. spontaneous speech), and time. Some phonetic features of ADS changed within the child's first year depending on gender and parental involvement/gender identity. Thus, further research on IDS needs to address also potential changes in ADS.

Exploring the Potential Impact of Sentence-Level Comprehension and Sentence-Level Fluency on Deaf Students' Passage Comprehension

2020 ◽  
Vol 63 (7) ◽  
pp. 2281-2292
Author(s):  
Ying Zhao ◽  
Xinchun Wu ◽  
Hongjun Chen ◽  
Peng Sun ◽  
Ruibo Xie ◽  
...  
Keyword(s):  
Independent Predictor ◽  
Vocabulary Knowledge ◽  
Group Differences ◽  
Regression Analyses ◽  
Deaf Students ◽  
Mediating Role ◽  
Sentence Level ◽  
Mediating Mechanisms ◽  
Potential Impact ◽  
The Relationship

Purpose This exploratory study aimed to investigate the potential impact of sentence-level comprehension and sentence-level fluency on passage comprehension of deaf students in elementary school. Method A total of 159 deaf students, 65 students ( M age = 13.46 years) in Grades 3 and 4 and 94 students ( M age = 14.95 years) in Grades 5 and 6, were assessed for nonverbal intelligence, vocabulary knowledge, sentence-level comprehension, sentence-level fluency, and passage comprehension. Group differences were examined using t tests, whereas the predictive and mediating mechanisms were examined using regression modeling. Results The regression analyses showed that the effect of sentence-level comprehension on passage comprehension was not significant, whereas sentence-level fluency was an independent predictor in Grades 3–4. Sentence-level comprehension and fluency contributed significant variance to passage comprehension in Grades 5–6. Sentence-level fluency fully mediated the influence of sentence-level comprehension on passage comprehension in Grades 3–4, playing a partial mediating role in Grades 5–6. Conclusions The relative contributions of sentence-level comprehension and fluency to deaf students' passage comprehension varied, and sentence-level fluency mediated the relationship between sentence-level comprehension and passage comprehension.

Natural products in complex microbiomes – Assembling multiple bacterial genomes directly through shotgun metagenomics

Planta Medica ◽  
2014 ◽  
Vol 80 (10) ◽  
Author(s):  
IJ Miller ◽  
T Weyna ◽  
C Mlot ◽  
SS Fong ◽  
K McPhail ◽  
...  
Keyword(s):  
Natural Products ◽  
Bacterial Genomes ◽  
Shotgun Metagenomics
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