Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.

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Resistance of natural waters within the Lake Baikal watershed to anthropogenic impacts

Geography and Natural Resources ◽

10.1134/s1875372815010060 ◽

2015 ◽

Vol 36 (1) ◽

pp. 40-47 ◽

Cited By ~ 3

Author(s):

O. V. Gagarinova

Keyword(s):

Lake Baikal ◽

Natural Waters ◽

Anthropogenic Impacts

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Reconstructing the baseline population structure of the exploited bivalve Arca noae in the Northern Adriatic Sea

10.5194/egusphere-egu21-7694 ◽

2021 ◽

Author(s):

Saskia Macharia ◽

Rafał Nawrot ◽

Michaela Berensmeier ◽

Ivo Gallmetzer ◽

Alexandra Haselmair ◽

...

Keyword(s):

Adriatic Sea ◽

Size Structure ◽

Anthropogenic Impacts ◽

Natural State ◽

Published Data ◽

Northern Adriatic Sea ◽

Important Species ◽

Northern Adriatic ◽

Shell Bed ◽

The Impact

The Northern Adriatic Sea is one of the most impacted ecosystems worldwide with a long history of anthropogenic impacts, ranging from overfishing and bottom trawling to eutrophication, deoxygenation and pollution. The impact of these multiple pressures on populations of economically important species is often difficult to evaluate due to paucity of long-term monitoring data. The edible bivalve Noah&#8217;s Ark shell (Arca noae L.) was intensively harvested in the eastern Adriatic Sea until 1949-1950 when it suffered a catastrophic population collapse due to unknown agents. The assessment of its subsequent recovery is hindered by the lack of data on the population size structure prior to that event. To reconstruct the natural baseline state of populations of A. noae before the onset of extensive harvesting, we studied fossil assemblages from two 1.5-m-long sediment cores collected in the southern Gulf of Trieste (off Piran, Slovenia), both recording the last ~9,500 years.The abundance and shell length of A. noae remained low in the lower part of the cores but increased strongly within the oyster-Arca shell bed corresponding to maximum flooding and early highstand sea-level phases (6,500-1,000 years ago). In contrasts, the top 8 cm of the core (the late highstand phase), marked by high concentration of pollutants and organic enrichment, contained only few and small (< 10 mm) A. noae shells. Moreover, no living individuals were found in grab samples taken from the two stations suggesting that the dense populations of A. noae, persisting there for several thousand years, were locally extirpated in the 20th century. To evaluate population recovery in other parts of the NE Adriatic, we compared the size distribution of fossil A. noae from the shell bed interval to the previously published data on living populations of this species sampled along Istrian peninsula between 1966 and 1978. Both fossil and extant populations were characterized by similar median size, modal size class and proportion of specimens > 50 mm (minimal legal landing size). These results suggest that within few decades after the 1949-1950 mass mortality event the size structure of populations of A. noae have largely returned to their earlier, natural state. The recovery was spatially variable, however, as attested by the decline of A. noae populations due to loss of suitable shell-bed habitats in the two studied stations off Piran.

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Abstract TP32: Endovascular Therapy for Acute Ischemic Stroke Beyond the 6 Hour Window

Stroke ◽

10.1161/str.48.suppl_1.tp32 ◽

2017 ◽

Vol 48 (suppl_1) ◽

Author(s):

Yi Mao ◽

Sameer Sharma ◽

Hesham Masoud ◽

Julius G Latorre

Keyword(s):

Ischemic Stroke ◽

Acute Ischemic Stroke ◽

Endovascular Therapy ◽

Current Data ◽

Posterior Circulation ◽

Published Data ◽

Advanced Imaging ◽

Poor Outcomes ◽

Mr Clean ◽

Insight Into

Background: Recent randomized trials demonstrated the efficacy of endovascular therapy (EVT) in managing acute ischemic stroke (AIS), though EVT was initiated <6 hours from time last seen well in nearly all patients, and posterior circulation strokes were excluded. Current data is limited for patients receiving EVT >6 hours, and more so for those with posterior circulation strokes. We aim to assess safety and clinical outcome of EVT in patients presenting >6 hours, with anterior or posterior circulation strokes. Methods: We conducted a retrospective review of patients with AIS receiving EVT >6 hours between 2012-2015, including those with unknown time of onset and wake-up strokes. Outcomes observed include mRS at ≥90 days, rates of recanalization (TICI 2b-3), sICH and mortality. Results: A total of 34 patients were identified presenting with AIS and receiving EVT >6 hours, including 25 anterior and 9 posterior circulation strokes. See Table 1 for comparison with published data from recent EVT trials. Conclusion: Our results are not significantly different from some of the recent trials. MR CLEAN, the only trial that did not employ advanced imaging in patient selection, had similar outcomes. The IV-tPA only groups of recent trials (where data is available) also produced comparable results. It should be noted that the patients in our study all have large vessel occlusions and high NIHSS, are mostly ineligible for tPA, and thus would be expected to have very poor outcomes without treatment. Our data supports the possibility of expanding the EVT window to >6 hours, and with advanced imaging screening, better rates of functional outcome/mortality may still be achieved. DAWN and DEFUSE3 trials currently underway should provide further insight into this subject.

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Northstar enables automatic classification of known and novel cell types from tumor samples

Scientific Reports ◽

10.1038/s41598-020-71805-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Fabio Zanini ◽

Bojk A. Berghuis ◽

Robert C. Jones ◽

Benedetta Nicolis di Robilant ◽

Rachel Yuan Nong ◽

...

Keyword(s):

Cell Types ◽

Neoplastic Cell ◽

Computational Approach ◽

Pancreatic Tumors ◽

Published Data ◽

Cell Type ◽

Disease Heterogeneity ◽

Manual Task ◽

Insight Into

Abstract Single cell transcriptomics is revolutionising our understanding of tissue and disease heterogeneity, yet cell type identification remains a partially manual task. Published algorithms for automatic cell annotation are limited to known cell types and fail to capture novel populations, especially cancer cells. We developed northstar, a computational approach to classify thousands of cells based on published data within seconds while simultaneously identifying and highlighting new cell states such as malignancies. We tested northstar on data from glioblastoma, melanoma, and seven different healthy tissues and obtained high accuracy and robustness. We collected eleven pancreatic tumors and identified three shared and five private neoplastic cell populations, offering insight into the origins of neuroendocrine and exocrine tumors. Northstar is a useful tool to assign known and novel cell type and states in the age of cell atlases.

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Insight into Biochemical Characterization of Plant Sesquiterpene Synthases

Analytical Chemistry Insights ◽

10.4137/aci.s40292 ◽

2016 ◽

Vol 11s1 ◽

pp. ACI.S40292

Author(s):

Tom Manczak ◽

Henrik Toft Simonsen

Keyword(s):

Kinetic Parameters ◽

Biochemical Characterization ◽

Radioactive Isotopes ◽

Published Data ◽

Enzymatic Characterization ◽

Turnover Number ◽

Terpene Synthases ◽

Thapsia Garganica ◽

Insight Into

A fast and reproducible protocol was established for enzymatic characterization of plant sesquiterpene synthases that can incorporate radioactivity in their products. The method utilizes the 96-well format in conjunction with cluster tubes and enables processing of >200 samples a day. Along with reduced reagent usage, it allows further reduction in the use of radioactive isotopes and flammable organic solvents. The sesquiterpene synthases previously characterized were expressed in yeast, and the plant-derived Thapsia garganica kunzeaol synthase TgTPS2 was tested in this method. KM for TgTPS2 was found to be 0.55 μM; the turnover number, kcat, was found to be 0.29 s−1, kcat for TgTPS2 is in agreement with that of terpene synthases of other plants, and kcat/ KM was found to be 0.53 s−1 μM−1 for TgTPS2. The kinetic parameters were in agreement with previously published data.

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Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Viruses ◽

10.3390/v11110979 ◽

2019 ◽

Vol 11 (11) ◽

pp. 979 ◽

Cited By ~ 127

Author(s):

Ping Liu ◽

Wu Chen ◽

Jin-Ping Chen

Keyword(s):

De Novo ◽

Sendai Virus ◽

Sequence Similarity ◽

Viral Metagenomics ◽

Manis Javanica ◽

Pathogenic Viruses ◽

Viral Communities ◽

High Level ◽

Viral Sequences ◽

Insight Into

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

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Analysis of the juvenile shell of Lingula anatina (Brachiopoda: Linguliformea) provides insight into the evolution of life cycles of fossil brachiopods

Paleobiology ◽

10.1017/pab.2020.51 ◽

2020 ◽

pp. 1-15

Author(s):

Anna A. Madison ◽

Tatyana V. Kuzmina ◽

Elena N. Temereva

Keyword(s):

Life Cycle ◽

Anterior Margin ◽

The Philippines ◽

Life Cycles ◽

Published Data ◽

Egg Envelope ◽

Evolution Of Life ◽

The Republic ◽

Planktotrophic Larvae ◽

Insight Into

Abstract Inferences on the development and morphology of extinct brachiopods must be informed by the ontogeny and shell ornamentation of extant brachiopods. Although the adult shells of extant brachiopods are well studied, detailed descriptions of the embryonic and juvenile shells of extant lingulides are lacking. Here, we describe in detail the shells of juveniles of Lingula anatina Lamarck, 1801 from Vietnam and the Republic of the Philippines. The following previously unknown properties of the lingulide shell are described: (1) a distinct border between the protegulum and the brephic shell; (2) drapes that develop on both the protegulum and brephic shell; and (3) the notched anterior margin of the brephic shell. The drapes and cogs on the brephic shell may be caused by the formation of setal follicles during the planktonic stage. Specimens of L. anatina from the Philippines have larger brephic shells than those from Vietnam, probably because the former have a longer planktonic stage. Based on comparisons of the first-formed shells of extant brachiopods with published data on fossil brachiopods, we suggest that the life cycle of extant lingulides, in which planktotrophic juveniles with a shell hatch from the egg envelope, is the most evolutionarily advanced brachiopod life cycle and appeared in the early Silurian. We suggest criteria for determining the type of life cycle based on the structure of the first-formed shell of brachiopods. Finally, we consider hypothetical scenarios of life cycles of fossil brachiopods, including true planktotrophic larvae in the Cambrian linguliforms.

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Genetic Diversity among Clostridium botulinum Strains Harboringbont/A2andbont/A3Genes

Applied and Environmental Microbiology ◽

10.1128/aem.02428-12 ◽

2012 ◽

Vol 78 (24) ◽

pp. 8712-8718 ◽

Cited By ~ 19

Author(s):

Carolina Lúquez ◽

Brian H. Raphael ◽

Lavin A. Joseph ◽

Sarah R. Meno ◽

Rafael A. Fernández ◽

...

Keyword(s):

Genetic Diversity ◽

Clostridium Botulinum ◽

Type A ◽

Gene Clusters ◽

Nucleotide Sequencing ◽

Toxin Gene ◽

Content Type ◽

Geographic Origins ◽

Diversity Studies ◽

Insight Into

ABSTRACTClostridium botulinumtype A strains are known to be genetically diverse and widespread throughout the world. Genetic diversity studies have focused mainly on strains harboring one type A botulinum toxin gene,bont/A1, although all reportedbont/Agene variants have been associated with botulism cases. Our study provides insight into the genetic diversity ofC. botulinumtype A strains, which containbont/A2(n= 42) andbont/A3(n= 4) genes, isolated from diverse samples and geographic origins. Genetic diversity was assessed by usingbontnucleotide sequencing, content analysis of thebontgene clusters, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Sequences ofbontgenes obtained in this study showed 99.9 to 100% identity with otherbont/A2orbont/A3gene sequences available in public databases. The neurotoxin gene clusters of the subtype A2 and A3 strains analyzed in this study were similar in gene content.C. botulinumstrains harboringbont/A2andbont/A3genes were divided into six and two MLST profiles, respectively. Four groups of strains shared a similarity of at least 95% by PFGE; the largest group included 21 out of 46 strains. The strains analyzed in this study showed relatively limited genetic diversity using either MLST or PFGE.

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La etología como herramienta para la conservación de fauna silvestre

Revista Colombiana de Ciencia Animal - RECIA ◽

10.24188/recia.v8.n0.2016.396 ◽

2016 ◽

Vol 8 ◽

pp. 391

Author(s):

ALCIDES SAMPEDRO MARÍN

Keyword(s):

Natural Selection ◽

Environmental Education ◽

Behavioral Ecology ◽

Biological Diversity ◽

Anthropogenic Impacts ◽

Adaptive Strategies ◽

The State ◽

Effective Size ◽

Darwinian Theory ◽

Living Organisms

The origins of ethology as a discipline are explained and is a proof of the Darwinian theory of the action of natural selection leading to the adaptive strategies that allow survival of living organisms. The emergence of behavioral ecology stands out as an important tool for the conservation of biological diversity. Its premises are explained, as well as several examples of behavior that affect the effective size of populations and anthropogenic impacts on various behaviors.Finally, the use of behavioral ecology as an indicator of the state of ecosystems and species and to develop environmental education is exemplified.

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The Role of Microbiome in Cancer Cell Stimulation and Therapy

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i51b33520 ◽

2021 ◽

pp. 97-115

Author(s):

Shahira Hassoubah

Keyword(s):

Immune Response ◽

Human Microbiome ◽

Future Research ◽

Published Data ◽

Disease States ◽

Life Threatening ◽

Indigenous Microbiota ◽

Symbiotic Microbiota ◽

Insight Into

In recent times, the microbiome has been increasingly recognized as having a hand in various disease states that include cancer as a part. Our commensal and symbiotic microbiota, in addition to pathogens with oncogenesis features, have tumor-suppressive characteristics. Our nutrition and other environmental influences can modulate some microbial species representatives within our digestive system and other systems. The microbiota has recently shown a two-way link to cancer immunotherapy for both the prognosis and the therapeutic aspects. Preclinical results indicated that microbiota modification could be transformed into a novel technique to improve cancer therapy's effectiveness. This article aimed to review recent development in our understanding of the microbiome and its relationship to cancer cells and discuss how the microbiome stimulates cancer and its clinical and therapeutic applications. Such information was selected and extracted from the PubMed, Web of Science, and Google Scholar databases for published data from 2000 to 2020 using relevant keywords containing a combination of terms, including the microbiome, cancer, immune response, immune response, and microbiota. Finally, we concluded that studying the human microbiome is necessary because it provides a thorough understanding of humans' interaction and their indigenous microbiota. The microbiome provides useful insight into future research studies to optimize these species to fight life-threatening diseases such as cancer and has rendered the microbiome a successful cancer treatment strategy.

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