scholarly journals Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea

2021 ◽  
Vol 12 ◽  
Author(s):  
Christos A. Christakis ◽  
Tamar Barkay ◽  
Eric S. Boyd
Keyword(s):  
Functional Dependence ◽  
Natural Habitat ◽  
Phylogenetic Reconstruction ◽  
Mercury Resistance ◽  
Future Research ◽  
Environmental Distribution ◽  
Bacterial Phyla ◽  
Mercury Compounds ◽  
Geothermal Environments ◽  
Lower Temperature

Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.

scholarly journals Evaluating the personality structure of semi-captive Asian elephants living in their natural habitat

2018 ◽  
Vol 5 (2) ◽  
pp. 172026 ◽  
Author(s):  
Martin W. Seltmann ◽  
Samuli Helle ◽  
Mark J. Adams ◽  
Khyne U Mar ◽  
Mirkka Lahdenperä
Keyword(s):  
Factor Analysis ◽  
Cognitive Abilities ◽  
Natural Habitat ◽  
Future Research ◽  
Personality Structure ◽  
Asian Elephants ◽  
Wild Mammals ◽  
Social Species ◽  
Explanatory Factor Analysis ◽  
Study Population

Data on personality for long-lived, highly social wild mammals with high cognitive abilities are rare. We investigated the personality structure of Asian elephants ( Elephas maximus ) by using a large sample of semi-captive timber elephants in Myanmar. Data were collected during 2014–2017 using questionnaires, for which elephant riders (mahouts) rated 28 behavioural adjectives of elephants. Repeated questionnaires were obtained for each elephant from several raters whenever possible, resulting in 690 ratings of 150 female and 107 male elephants. We started by performing a confirmatory factor analysis to compare the fit of our data to a previously published captive elephant personality structure. Owing to a poor fit of this model to our data, we proceeded by performing explanatory factor analysis to determine the personality structure in our study population. This model suggested that personality in these elephants was manifested as three factors that we labelled as Attentiveness, Sociability and Aggressiveness. This structure did not differ between the sexes. These results provide the basis for future research on the link between personality and reproductive success in this endangered species and more generally, help to resolve the selective pressures on personalities in long-lived, highly social species.

scholarly journals Experiences from City-Scale Simulation of Thermal Grids

Resources ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 10
Author(s):  
Johan Simonsson ◽  
Khalid Tourkey Atta ◽  
Gerald Schweiger ◽  
Wolfgang Birk
Keyword(s):  
Renewable Energy Sources ◽  
District Heating ◽  
Lessons Learned ◽  
Spatial Behavior ◽  
Future Research ◽  
Heating And Cooling ◽  
Box Models ◽  
Future Research Directions ◽  
Lower Temperature

Dynamic simulation of district heating and cooling networks has an increased importance in the transition towards renewable energy sources and lower temperature district heating grids, as both temporal and spatial behavior need to be considered. Even though much research and development has been performed in the field, there are several pitfalls and challenges towards dynamic district heating and cooling simulation for everyday use. This article presents the experiences from developing and working with a city-scale simulator of a district heating grid located in Luleå, Sweden. The grid model in the case study is a physics based white-box model, while consumer models are either data-driven black-box or gray-box models. The control system and operator models replicate the manual and automatic operation of the combined heat and power plant. Using the functional mock-up interface standard, a co-simulation environment integrates all the models. Further, the validation of the simulator is discussed. Lessons learned from the project are presented along with future research directions, corresponding to identified gaps and challenges.

scholarly journals Pengaruh pH dan Suhu terhadap Aktivitas Pereduksi Merkuri Bakteri Resisten Merkuri Tinggi Bacillus cereus yang Diisolasi dari Urin Pasien dengan Amalgam Gigi

e-GIGI ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Billy J. Kepel ◽  
Widdhi Bodhi ◽  
. Fatimawali
Keyword(s):  
Bacillus Cereus ◽  
Incubation Temperature ◽  
Mercury Resistance ◽  
Resistant Bacteria ◽  
Growth Media ◽  
Mercury Compounds ◽  
Reducing Activity ◽  
Mercury Detoxification ◽  
Incubation Temperatures ◽  
Mercury Resistant Bacteria

Abstract: Mercury is a very toxic compound to humans, therefore, a method to overcome its presence in the environment is required. Detoxification of mercury can be done by using mercury resistant bacteria. Mercury-resistant bacteria Bacillus cereus isolate FUA have been obtained from the urine of patients with dental mercury amalgam. This study was aimed to determine the mercury detoxification activity of Bacillus cereus isolate FUA at varying pH medium and incubation temperature. The study was carried out by growing Bacillus cereus isolate FUA on oblique media, then were planted in the growth media of LB broth containing mercury compounds of 10 ppm HgCl2 with varying pHs of 5, 7, and 9 and incubation temperatures of 15, 25 and 35oC. The amount of bacterial growth was analyzed by using spectrophotometer and mercury levels were analyzed by using CV-AAS method. The results showed that the growth and mercury reducing activity of Bacillus cereus isolate FUA were optimum at pH 7 and incubation temperature of 35oC. In conclusion, the growth of Bacillus cereus isolate FUA and its mercury reducing activity were optimum at pH 7 and temperature of 35oC. It is expected that the results of this study can be the basis for further research on the process of mercury detoxificationKeywords: Bacillus cereus, urine, mercury resistance, pH, temperature Abstrak: Merkuri adalah senyawa yang sangat beracun bagi manusia sehingga diperlukan metode untuk mengatasi keberadaannya di lingkungan. Detoksifikasi merkuri dapat dilakukan dengan menggunakan bakteri resisten merkuri. Bakteri yang resisten merkuri Bacillus cereus isolat FUA telah diperoleh dari urin pasien dengan amalgam gigi. Penelitian ini bertujuan untuk mengetahui aktivitas detoksifikasi merkuri Bacillus cereus isolat FUA pada berbagai variasi pH medium dan suhu inkubasi. Bakteri Bacillus cereus isolat FUA ditumbuhkan pada media miring, kemudian ditanam pada media pertumbuhan bakteri LB broth yang mengandung senyawa merkuri 10 ppm HgCl2 dengan berbagai pH 5, 7 dan 9 dan suhu inkubasi 15, 25 dan 35oC. Jumlah pertumbuhan bakteri dianalisis menggunakan spektrofotometer dan kadar merkuri dianalisis menggunakan metode CV-AAS. Hasil penelitian menunjukkan bahwa aktivitas pertumbuhan dan aktivitas pereduksi merkuri Bacillus cereus isolat FUA optimum pada lingkungan pertumbuhan dengan pH 7 dan suhu inkubasi 35oC. Simpulan penelitian ini ialah aktivitas pertumbuhan dan pereduksi merkuri Bacillus cereus isolat FUA yang optimum pada pH 7 dan suhu 35oC. Diharapkan hasil penelitian ini dapat menjadi dasar untuk penelitian lebih lanjut tentang proses detoksifikasi merkuri.Kata kunci: Bacillus cereus, urin, resistensi merkuri, pH, suhu

scholarly journals Plant Age Influences Microbiome Communities More Than Plant Compartment in Greenhouse Grown Creeping Bentgrass

2021 ◽  
Author(s):  
Joseph Doherty ◽  
Jo Anne Crouch ◽  
Joseph Roberts
Keyword(s):  
Community Structure ◽  
Management Practices ◽  
Community Dynamics ◽  
Surface Characteristics ◽  
Creeping Bentgrass ◽  
Plant Age ◽  
Plant Health ◽  
Future Research ◽  
Bacterial Phyla ◽  
Fungal Community Structure

Creeping bentgrass (Agrostis stolonifera L.) is widely used in golf course settings for its desirable playing surface characteristics, however it is highly susceptible to diseases that can disrupt surface integrity and cause significant losses despite preventative management. Understanding the influence of early plant growth and basic management practices on microbiome communities are crucial first steps to developing future efforts to harness the microbiome for plant health. This study investigated bacterial and fungal communities of creeping bentgrass foliage and rhizosphere through six months post-emergence under a controlled environment to elucidate microbiome community dynamics in response to plant age. We hypothesized that plant compartments will host distinct community structures and exhibit different responses to plant age. Our results showed that predominant bacterial phyla and fungal classes remain consistent across time and plant compartment. However, genus level classification revealed bacterial taxa differed across plant compartment while fungal taxa remained consistent. Host influence over the microbiome manifests quickly, with the largest shift in both microbial communities occurring between emergence and two months post-emergence. For example, Burkholderia and Penicillium were present at high relative abundance at emergence, but by two months post-emergence both taxa decreased significantly. Bacterial communities continued to experience significant fluctuation in rare taxa from two months post-emergence onward, while fungal community structure was driven by the fluctuation of the most common taxa. These results highlight the connection between plant age and microbial community structure in creeping bentgrass in addition to underscoring future research efforts in creeping bentgrass microbiome manipulation for plant health.

scholarly journals Repeated Evaluations of Testes and Semen Characteristics in Two Binturongs (Arctictis binturong)

2021 ◽  
Vol 8 ◽  
Author(s):  
Zainal Zahari Zainuddin ◽  
Symphorosa Sipangkui ◽  
Mohd Farqhan Kelana ◽  
Yap Keng Chee ◽  
Mohamed Reza Mohamed Tarmizi ◽  
...  
Keyword(s):  
Natural Habitat ◽  
Ex Situ ◽  
Future Research ◽  
Medium Size ◽  
Research Report ◽  
Adult Males ◽  
Semen Characteristics ◽  
Reproductive Techniques ◽  
Secondary Objective ◽  
Conservation Breeding

The binturong is a medium size carnivore belonging to the Viverrid family that lives in dense forests of South-East Asia. In addition to the protection of this vulnerable species in its natural habitat (in situ), conservation breeding efforts (ex situ) aim at maintaining a good genetic diversity while increasing the number of individuals to reinforce wild populations. Both approaches require a solid understanding of binturong's basic biology. However, there is still a lack of precise information about reproduction. The objective of this brief research report was to analyze testicular sizes and semen characteristics at different times of the year to better understand the reproductive physiology and inform future conservation efforts. A secondary objective was to describe sperm cryotolerance for the first time in that species. Examinations of testes and semen collections were conducted on two adult males. While testicular measurements were relatively constant across multiple examinations, semen characteristics (volume, viability, sperm concentrations, sperm motility) varied between samples. However, incidence of sperm morphological abnormalities was consistently high. Sperm cryotolerance appeared to be poor but further studies are warranted. The present dataset will be useful for future research on binturong reproduction and for the development of assisted reproductive techniques and biobanking of germplasms in that species.

scholarly journals Cortinarius pakistanicus and C. pseudotorvus: two new species in oak forests in the Pakistan Himalayas

MycoKeys ◽  
2020 ◽  
Vol 74 ◽  
pp. 91-108
Author(s):  
Arooj Naseer ◽  
Isaac Garrido-Benavent ◽  
Junaid Khan ◽  
Josep Ballarà ◽  
Rafael Mahiques ◽  
...  
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Future Research ◽  
Oak Forests ◽  
High Mountain ◽  
Sem Images ◽  
Integrative Framework ◽  
Tree Inference ◽  
Molecular Phylogenetic

The genus of basidiomycetous fungiCortinarius occurs worldwide, from subtropical to boreal latitudes. Although molecular systematics has triggered the study of these fungi in the Americas and Europe in the last two decades, there is still limited research on its diversity in large portions of the planet, such as the high mountain ranges of Asia. Several collections of Cortinarius were made during mycological field trips conducted between 2014 and 2018 in pure oak forests in the Pakistan Himalayas. An integrative framework combining morphological and phylogenetic data was employed for their study. As a result, the two species C. pakistanicus and C. pseudotorvus are here described as new to science. Detailed macro- and micro-morphological descriptions, including SEM images of spores, and a molecular phylogenetic reconstruction based on nrITS sequence data are provided and used to discriminate the new species from morphologically and phylogenetically close taxa. Whereas our phylogenetic tree inference gave unequivocal support for the inclusion of C. pseudotorvus within C. sect. Telamonia, the assignment of C. pakistanicus to any known sections remained elusive. These species likely establish ectomycorrhizal associations with trees in the genus Quercus, making this type of forest in the Pakistan Himalayas a promising focus for future research on the diversity of Cortinarius.

scholarly journals phoDAlkaline Phosphatase Gene Diversity in Soil

2015 ◽  
Vol 81 (20) ◽  
pp. 7281-7289 ◽  
Author(s):  
Sabine A. Ragot ◽  
Michael A. Kertesz ◽  
Else K. Bünemann
Keyword(s):  
Alkaline Phosphatase ◽  
Bacterial Community Structure ◽  
Gene Diversity ◽  
Organic Phosphorus ◽  
454 Sequencing ◽  
Environmental Distribution ◽  
Content Type ◽  
Bacterial Phyla ◽  
Operational Taxonomic Units ◽  
Different Climates

ABSTRACTPhosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution ofphoDgenes using whole-genome and metagenome databases.phoDalkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity ofphoD, we developed a new set of primers which targetsphoDgenes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 differentphoDoperational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalentphoDgenes identified in these soils were affiliated with the ordersActinomycetales(13 to 35%),Bacillales(1 to 29%),Gloeobacterales(1 to 18%),Rhizobiales(18 to 27%), andPseudomonadales(0 to 22%). The primers also amplifiedphoDgenes from additional orders, includingBurkholderiales,Caulobacterales,Deinococcales,Planctomycetales, andXanthomonadales, which represented the major differences inphoDcomposition between samples, highlighting the singularity of each community. Additionally, thephoDbacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity ofphoDin soil and represent a valuable tool for the study ofphoDalkaline phosphatase in environmental samples.

Specific heat capacity of wood between −140 and 50 °C in dry and wet state

Holzforschung ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Martin Nopens ◽  
Uta Sazama ◽  
Andreas Krause ◽  
Michael Fröba
Keyword(s):  
Heat Capacity ◽  
Specific Heat ◽  
Specific Heat Capacity ◽  
Moisture Transfer ◽  
Bound Water ◽  
Future Research ◽  
Scanning Calorimetry ◽  
Fundamental Research ◽  
Liquid Nitrogen Cooling ◽  
Lower Temperature

Abstract Specific heat capacity of wood is an important material property for fundamental research and timber technology. However, the existing database for heat capacity values is limited, especially for data below 0 °C. Therefore, the aim of this study was to investigate the specific heat capacity of wood with different moisture contents (dry, below and above fibre saturation) in lower temperature. Beech (Fagus sylvatica) and scots pine (Pinus sylvestris) were investigated via differential scanning calorimetry (DSC), equipped with a liquid nitrogen-cooling device, using the sapphire standard. Specific heat capacity for beech and pine were linear within the investigated temperature region. Values above 0 °C are in agreement with existing literature. Both species showed similar results. Based on the obtained results the specific heat capacity for bound water was calculated. The presented results are an important step for increasing the database of wood heat capacity. These findings enable future research for calculating heat-flux, diffusion and moisture transfer in wood.

scholarly journals Supertrees based on the subtree prune-and-regraft distance

2013 ◽  
Author(s):  
Chris Whidden ◽  
Norbert Zeh ◽  
Robert G Beiko
Keyword(s):  
Gene Transfer ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Optimality Criteria ◽  
Gene Trees ◽  
Long Distance ◽  
Bacterial Phyla ◽  
Benchmark Datasets ◽  
Spr Distance ◽  
Subtree Prune And Regraft

Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of simulated benchmark datasets, we show that SPR supertrees are more similar to correct species histories under plausible rates of LGT than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera; a small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT.

scholarly journals Supertrees based on the subtree prune-and-regraft distance

2013 ◽  
Author(s):  
Chris Whidden ◽  
Norbert Zeh ◽  
Robert G Beiko
Keyword(s):  
Gene Transfer ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Optimality Criteria ◽  
Gene Trees ◽  
Long Distance ◽  
Bacterial Phyla ◽  
Benchmark Datasets ◽  
Spr Distance ◽  
Subtree Prune And Regraft

Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of simulated benchmark datasets, we show that SPR supertrees are more similar to correct species histories under plausible rates of LGT than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera; a small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT.

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