scholarly journals The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuki Hongo ◽  
Kei Kimura ◽  
Yoshihiro Takaki ◽  
Yukari Yoshida ◽  
Shuichiro Baba ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Environmental Conditions ◽  
Phaeodactylum Tricornutum ◽  
Evolutionary Relationship ◽  
Thalassiosira Pseudonana ◽  
Gene Fragment ◽  
Ssdna Virus ◽  
Endogenous Virus ◽  
The World ◽  
Long Interspersed Nuclear Element

AbstractDiatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can coexist with infectious viruses during blooms. To further understand this relationship, we sequenced the C. tenuissimus strain NIES-3715 genome. A gene fragment of a replication-associated gene from the infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated into each 41 Mb of haploid assembly. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. Additionally, retrotransposon genes possessing a reverse transcriptase function were more abundant in C. tenuissimus than in Thalassiosira pseudonana and Phaeodactylum tricornutum. Moreover, a target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study provides further insights into the diatom-virus evolutionary relationship.

scholarly journals Endogenization of ssDNA fragment from an infectious virus in the genome of the Chaetoceros tenuissimus

2021 ◽  
Author(s):  
Yuki Hongo ◽  
Kei Kimura ◽  
Yoshihiro Takaki ◽  
Yukari Yoshida ◽  
Shuichiro Baba ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Viral Infection ◽  
Infectious Virus ◽  
Evolutionary Relationship ◽  
Target Site Duplication ◽  
Gene Fragment ◽  
Ssdna Virus ◽  
Endogenous Virus ◽  
Genome Information ◽  
Long Interspersed Nuclear Element

Abstract One of the smallest diatoms, Chaetoceros tenuissimus, maintains their population despite coexisting with infectious viruses during blooms. To further understand this relationship, here, we sequenced the C. tenuissimus NIES-3715 genome. A gene fragment of a replication-associated gene from its own infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated in a total of 41 Mbp of both haploid assemblies. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. A target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study used genome information provides further insights into the diatom-virus evolutionary relationship.

scholarly journals Molecular Systematic Investigations of Three Fin Fish Cichlid Species of Oreochromis niloticus (Nile Tilapia), Genetically Improved Farmed Tilapia (GIFT) and Astronotus ocellatus (Oscar Cichlid)

2021 ◽  
Vol 10 (4) ◽  
pp. 2850-2860
Keyword(s):  
Phylogenetic Tree ◽  
Nile Tilapia ◽  
Evolutionary Relationship ◽  
Aquatic Organisms ◽  
Recent Common Ancestor ◽  
Farmed Fish ◽  
Molecular Systematic ◽  
Cichlid Species ◽  
Astronotus Ocellatus ◽  
The World

Fisheries in India contribute significantly to the total GDP of agriculture and earn significant foreign exchange. Aquaculture is playing an important role in India and is bestowed with a huge biodiversity of aquatic organisms. India ranks second in total fish production in the world. Nile tilapia has become the world’s second most popular farmed fish, after carps. Oscars is a popular aquarium fish around the world. In the present study, efforts were made to analyze the extent of divergence or similarity among three cichlid finfishes (Nile Tilapia, GIFT Tilapia, and Oscar Cichlid) using molecular biology techniques such as Random Amplification of Polymorphic DNA (RAPD) and Restriction Fragment Length Polymorphism (RFLP). The Phylogenetic tree was constructed using PhyElph software to study the evolutionary relationship between the three cichlid finfish species. The Phylogenetic or evolutionary relationship was established for the three fishes, Nile tilapia, GIFT, and Oscar cichlid, with the Phylogenetic tree. It was found that Nile tilapia and GIFT share a recent common ancestor, while Oscar cichlid does not share any evolutionary relationship with Nile tilapia and GIFT.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

scholarly journals The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jan Pyrih ◽  
Vojtěch Žárský ◽  
Justin D. Fellows ◽  
Christopher Grosche ◽  
Dorota Wloga ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Complex I ◽  
Phaeodactylum Tricornutum ◽  
Tetrahymena Thermophila ◽  
Thalassiosira Pseudonana ◽  
Cellular Distribution ◽  
Iron Sulfur Cluster ◽  
Iron Sulfur ◽  
Secondary Plastids ◽  
Respiratory Complex I

Abstract Background Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions. Results We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either α-proteobacterial or cyanobacterial endosymbionts. Conclusion Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans).

Kuehneola loeseneriana.

2021 ◽  
Author(s):  
Keyword(s):  
South America ◽  
Environmental Conditions ◽  
Pathogenic Fungus ◽  
North Central ◽  
Plant Pathogenic Fungus ◽  
The World ◽  
Agricultural Plants

Abstract There is little published information on this plant pathogenic fungus, which is limited to parts of North, Central and South America. It infects Rubus spp., which exist in other regions of the world with similar environmental conditions, therefore this species may pose a threat to native or agricultural plants if introduced.

A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

2021 ◽  
Vol 9 (1) ◽  
pp. 49-55
Author(s):  
Vanlal hruaia ◽  
◽  
Lal rinmuana ◽  
J Lalbiaknunga ◽  
Laldinfeli Ralte
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Flowering Plants ◽  
Morphological Features ◽  
Total Evidence ◽  
Pictorial Representation ◽  
Phenetic Analysis ◽  
Morphological Relationship

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

scholarly journals Confusion and Panic: Health & Environment

1970 ◽  
pp. 9
Author(s):  
Lebanese American University
Keyword(s):  
Natural Resources ◽  
Environmental Conditions ◽  
Health Conditions ◽  
Health Food ◽  
Health Concerns ◽  
Life Saving ◽  
The World

Health concerns have gained proportional attention among the peoples and governments of the world. Or at least it looks that way! Terms like Cholesterol, Triglyceride, Diabetes, Tumor, Benign, Malignant are all too familiar to many. Health food and diets have mushroomed into large money making industries. I wonder if they are life-saving too! Furthermore, it is becoming more difficult to separate between health and environment. Hence, the deterioration of health conditions all over the world is closely associated to impairments in environmental conditions and natural resources.

scholarly journals Spatio-temporal patterns of the oceanic conditions and nearshore marine community in the Mid-Atlantic Bight (New Jersey, USA)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7927 ◽  
Author(s):  
Juan C. Levesque
Keyword(s):  
New Jersey ◽  
Dissolved Oxygen ◽  
Water Temperature ◽  
Environmental Conditions ◽  
Clupea Harengus ◽  
Sediment Type ◽  
Temperature Preference ◽  
Marine Fauna ◽  
The World ◽  
Marine Community

Oceanic environmental conditions influence, shape, and control the geographical range, spatial distribution, abundance, and size composition of marine fauna. Water temperature, salinity, dissolved oxygen, depth, and sediment type influence select fish life-history characteristics and community structure. Marine communities are vulnerable to major changes in environmental conditions, but the response and severity depends on various biological or ecological factors, such as resilience to stress or adaptation. Researchers around the world have predicted and documented numerous alterations in fish communities caused by ongoing significant physicochemical shifts associated with natural and potentially unnatural sources, but published studies describing the historical conditions are lacking for most regions around the world, including the coastal waters off New Jersey. Given the need to understand these processes, a multifaceted investigation was undertaken to describe, evaluate, and compare the oceanic conditions and nearshore marine fauna community off New Jersey during 1988 through 2015. Findings showed the oceanic conditions varied over time and space. Mean surface water temperature increased significantly about 0.6 °C per decade, mean salinity decreased about 1.3 psu per decade, and dissolved oxygen increased 0.09 mg/l per decade. Over 20.4 million fish and invertebrates (1,338.3 mt) representing 214 (water temperature preference classified) species (not including unidentified species) were collected within 15 strata (areas: 12−26) off the coast of New Jersey from 1988 to 2015. Three marine fauna water temperature preference groups (coldwater-adapted, warmwater-adapted, and subtropic-adapted) were identified in the study area. The main coldwater-adapted species collected were longfin squid (Loligo pealei) (n = 2, 225, 975), Atlantic herring (Clupea harengus) (n = 544, 032), and little skate (Leucoraja erinacea) (n = 316, 356), while Atlantic butterfish (Peprilus triacanthus) (n = 2, 873, 138), scup (Stenotomus chrysops) (n = 1, 318, 569), and northern searobin (Prionotus carolinus) (n = 503, 230) represented the warmwater-adapted group. Bay anchovy (Anchoa mitchilli) (n = 9, 227, 960), striped anchovy (Anchoa hepsetus) (n = 245, 214), and Atlantic moonfish (Vomer setapinnis) (n = 38, 691) denoted the subtropic-adapted group. Subtropic-adapted species were the most abundant and coldwater-adapted were the least abundant water temperature preference group. The estimated abundance of coldwater-adapted species declined, warmwater-adapted species slightly increased, and subtropic-adapted species decreased with time, which suggest the environmental conditions are influencing and thereby shifting the marine community.

scholarly journals Relationship Between Scorpion Stings Events and Environmental Conditions in Mainland France

2021 ◽  
Author(s):  
Jules-Antoine Vaucel ◽  
Sébastien Larréché ◽  
Camille Paradis ◽  
Magali Labadie ◽  
Arnaud Courtois ◽  
...  
Keyword(s):  
North Africa ◽  
Environmental Conditions ◽  
Mediterranean Coast ◽  
Poison Control ◽  
Flow Temperature ◽  
The World ◽  
Scorpion Stings ◽  
Multi Center Study ◽  
The Impact ◽  
Amazonian Region

Abstract In the world, the impact of environmental conditions on the number of scorpion events was evaluated in North Africa,Middle East, and the Amazonian region but not in Europe. In mainland France, scorpion species described are Buthus occitanus (Amoreux, 1789), Belisarius xambeui (Simon, 1879) and 4 Euscorpiidae: Euscorpius concinnus (Koch, 1837), Euscorpius italicus (Herbst, 1800), Euscorpius tergestinus (Koch, 1837), and Tetratrichobothrius flavicaudis (De Geer, 1778). We aimed to describe the impact of environmental conduction on the number of scorpion events. For this, a retrospective multi-center study was conducted with data from the French poison control centers files about scorpion events between 1 January 2011 and 31 December 2020. During the study period, 975 incoming calls for scorpion events were recorded and 574 were related to scorpions native to mainland France and Corsica: B. occitanus (n = 86), Euscorpiidae species (n = 222), B. xambeui (n = 1), and undetermined species (n = 265). Cases were mostly reported along the Mediterranean coast, along rivers, and in cities with a trading port. The number of scorpion events was linked to the rivers' water level, rivers' flow, temperature, sunshine, and pluviometry (P < 0.05 for all variables). B. occitanus need warmest and driest environment than Euscorpiidae spp. A link between the severity of the envenoming and climatic condition or seasonality was not demonstrated.

scholarly journals Overexpression of key sterol pathway enzymes in two model marine diatoms alters sterol profiles in Phaeodactylum tricornutum

2020 ◽  
Author(s):  
Ana Cristina Jaramillo-Madrid ◽  
Raffaela Abbriano ◽  
Justin Ashworth ◽  
Michele Fabris ◽  
Peter J. Ralph
Keyword(s):  
Intracellular Signaling ◽  
Phaeodactylum Tricornutum ◽  
Metabolic Flux ◽  
Total Sterol ◽  
Sterol Composition ◽  
Thalassiosira Pseudonana ◽  
Squalene Epoxidase ◽  
End Point ◽  
Eukaryotic Phytoplankton ◽  
Coa Reductase

AbstractSterols are a class of triterpenoid molecules with diverse functional roles in eukaryotic cells, including intracellular signaling and regulation of cell membrane fluidity. Diatoms are a dominant eukaryotic phytoplankton group that produce a wide diversity of sterol compounds. The enzymes 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) and squalene epoxidase (SQE) have been reported to be rate-limiting steps in sterol biosynthesis in other model eukaryotes; however, the extent to which these enzymes regulate triterpenoid production in diatoms is not known. To probe the role of these two metabolic nodes in the regulation of sterol metabolic flux in diatoms, we independently over-expressed two versions of the native HMGR and a conventional, heterologous SQE gene in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. Overexpression of these key enzymes resulted in significant differential accumulation of downstream sterol pathway intermediates in P. tricornutum. HMGR-mVenus overexpression resulted in the accumulation of squalene, cycloartenol, and obtusifoliol, while cycloartenol and obtusifoliol accumulated in response to heterologous NoSQE-mVenus overexpression. In addition, accumulation of the end-point sterol 24-methylenecholesta-5,24(24’)-dien-3β-ol was observed in all P. tricornutum overexpression lines, and campesterol increased 3-fold in P. tricornutum lines expressing NoSQE-mVenus. Minor differences in end-point sterol composition were also found in T. pseudonana, but no accumulation of sterol pathway intermediates was observed. Despite the successful manipulation of pathway intermediates and individual sterols in P. tricornutum, total sterol levels did not change significantly in transformed lines, suggesting the existence of tight pathway regulation to maintain total sterol content.

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