The virus integrations in gut microbes associated with dysbiosis of microbial community in tumorigenesis of colorectal carcinoma

AbstractPatients with colorectal cancer (CRC) have a different gut microbial and viral communities from healthy individuals. But little is known about the ways and functions of interaction of virus-bacteria, let alone its correlation with the aetiology of CRC. In this study we aimed to identify the association between the genetic integration of virusbacteria and the expansion of some microbial population during tumorigenesis of human colorectum. Using a gut metagenomics sequencing data of healthy controls, advanced adenoma and carcinoma patients, to our knowledge, we demonstrate for the first time that the viral genetic integrations in gut microbes tend to occur in CRC patients and are potentially associated with the carcinogenesis. We found that almost all of the genetic integrations were happened between bacteriophages and bacteria, which could be influenced by the abundance of the phage communities. Importantly, the integrations of phage-carried positive effective genes offered selective advantages to the commensal and potential pathogenic bacteria, as a result, potentially led to a microbial dysbiosis along with the increasing bacterial diversity in carcinoma patients. Consequently, our work opens a new way to understand the carcinogenicity in complex intestinal ecosystems.

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Y/X-Chromosome-Bearing Sperm Shows Elevated Ratio in the Left but Not the Right Testes in Healthy Mice

Life ◽

10.3390/life11111219 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1219

Author(s):

Chengqing Hu ◽

Jiangcheng Shi ◽

Yujing Chi ◽

Jichun Yang ◽

Qinghua Cui

Keyword(s):

Flow Cytometry ◽

X Chromosome ◽

Sequencing Data ◽

Left Testis ◽

Mirna Sequencing ◽

The Right ◽

Almost All ◽

Multicellular Organisms ◽

First Time ◽

Lower Expression

The sex chromosomes play central roles in determining the sex of almost all of the multicellular organisms. It is well known that meiosis in mammalian spermatogenesis produces ~50% Y- and ~50% X-chromosome-bearing sperm, a 1:1 ratio. Here we first reveal that the X-chromosome-encoded miRNAs show lower expression levels in the left testis than in the right testis in healthy mice using bioinformatics modeling of miRNA-sequencing data, suggesting that the Y:X ratio could be unbalanced between the left testis and the right testis. We further reveal that the Y:X ratio is significantly elevated in the left testis but balanced in the right testis using flow cytometry. This study represents the first time the biased Y:X ratio in the left testis but not in the right testis is revealed.

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Deciphering the effects of kosmotrope and chaotrope salts during aqueous two phase extraction (ATPE) of polyphenolic compounds and glycoalkaloids from the leaves of a nutraceutical plant, Solanum retroflexum, with the aid of UPLC-QTOF-MS

Applied Biological Chemistry ◽

10.1186/s13765-021-00603-8 ◽

2021 ◽

Vol 64 (1) ◽

Author(s):

Tebogo Mokgehle ◽

Ntakadzeni Madala ◽

Wilson Gitari ◽

Nikita Tavengwa

Keyword(s):

Polar Compounds ◽

Ultra Performance Liquid Chromatography ◽

Polyphenolic Compounds ◽

Phase Extraction ◽

Two Phase ◽

Solanum Retroflexum ◽

Chaotropic Salts ◽

Almost All ◽

First Time ◽

Aqueous Two Phase Extraction

AbstractSolanum plants (Solanaceae) are renowned source of nutraceuticals and have widely been explored for their phytochemical constituents. This work investigated the effects of kosmotropic and chaotropic salts on the number of phytochemicals extracted from the leaves of a nutraceutical plant, Solanum retroflexum, and analyzed on the ultra-performance liquid chromatography hyphenated to a quadrupole time of flight mass spectrometer (UPLC-QTOF-MS) detector. Here, a total of 20 different compounds were putatively characterized. The majority of the identified compounds were polyphenols and glycoalkaloids. Another compound, caffeoyl malate was identified for the first time in this plant. Glycoalkaloids such as solanelagnin, solamargine, solasonine, β-solanine (I) and β-solanine (II) were found to be extracted by almost all the salts used herein. Kosmotrope salts, overall, were more efficient in extracting polar compounds with 4 more polyphenolic compounds extracted compared to the chaotropes. Chaotropes were generally more selective for the extraction of less polar compounds (glycoalkaloids) with 3 more extracted than the kosmotropes. The chaotrope and the kosmotrope that extracted the most metabolites were NaCl and Na2SO4, respectively, with 12 metabolites extracted for each salt. This work demonstrated that a comprehensive metabolome of S. retroflexum, more than what was previously reported on the same plant, can be achieved by application of kosmotropes and chaotropes as extractants with the aid of the Aqueous Two Phase Extraction approach. The best-performing salts, Na2SO4 or NaCl, could potentially be applied on a commercial scale, to meet the ever-growing demand of the studied metabolites. The Aqueous Two Phase Extraction technique was found to be efficient in simultaneous extraction of multiple metabolites which can be applied in metabolomics.

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Comparison on the Nutrient Plunder Capacity of Orychophragmus violaceus and Brassica napus L. Based on Electrophysiological Information

Horticulturae ◽

10.3390/horticulturae7080206 ◽

2021 ◽

Vol 7 (8) ◽

pp. 206

Author(s):

Cheng Zhang ◽

Yue Su ◽

Yanyou Wu ◽

Haitao Li ◽

Ying Zhou ◽

...

Keyword(s):

Brassica Napus ◽

Orychophragmus Violaceus ◽

Nutrient Metabolism ◽

Brassica Napus L ◽

Adaptive Mechanisms ◽

Capacitive Reactance ◽

Time Determination ◽

Almost All ◽

First Time

The nutrient metabolism, growth and development of plants are strongly affected by its nutrient plunder, and plants have different adaptive mechanisms to low-nutrient environments. The electrophysiological activities involve almost all life processes of plants. In this study, the active transport flow of nutrient (NAF) and nutrient plunder capacity (NPC) of plants were defined based on leaf intrinsic impedance (IZ), capacitive reactance (IXc), inductive reactance (IXL) and capacitance (IC) to evaluate the nutrient plunder capacity of plants for the first time. The results indicate that Orychophragmus violaceus had higher (p < 0.01) NPC and IC and lower (p < 0.01) IR, IXc, IXL and IZ as compared to Brassica napus L., which supports a superior ion affinity and that it could be better adapted to low-nutrient environments. UAF and NPC of plants exhibited good correlations with crude protein, crude ash and water content, and precisely revealed the plunder capacity and adaptive strategies of plants to nutrients. The present work highlights that O. violaceus had superior NPC and ion affinity compared with B. napus, and provided a novel, rapid, reliable method based on the plant’s electrophysiological information for real-time determination of the nutrient plunder capacity of plants.

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Isolation and Characterization of Bacteriophage ZCSE6 against Salmonella spp.: Phage Application in Milk

Biologics ◽

10.3390/biologics1020010 ◽

2021 ◽

Vol 1 (2) ◽

pp. 164-176

Author(s):

Abdallah S. Abdelsattar ◽

Anan Safwat ◽

Rana Nofal ◽

Amera Elsayed ◽

Salsabil Makky ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Raw Milk ◽

Salmonella Spp ◽

Isolation And Characterization ◽

Food Borne ◽

Wide Range ◽

Almost All ◽

And Control ◽

Milk And Dairy Products

Food safety is very important in the food industry as most pathogenic bacteria can cause food-borne diseases and negatively affect public health. In the milk industry, contamination with Salmonella has always been a challenge, but the risks have dramatically increased as almost all bacteria now show resistance to a wide range of commercial antibiotics. This study aimed to isolate a bacteriophage to be used as a bactericidal agent against Salmonella in milk and dairy products. Here, phage ZCSE6 has been isolated from raw milk sample sand molecularly and chemically characterized. At different multiplicities of infection (MOIs) of 0.1, 0.01, and 0.001, the phage–Salmonella interaction was studied for 6 h at 37 °C and 24 h at 8 °C. In addition, ZCSE6 was tested against Salmonella contamination in milk to examine its lytic activity for 3 h at 37 °C. The results showed that ZCSE6 has a small genome size (<48.5 kbp) and belongs to the Siphovirus family. Phage ZCSE6 revealed a high thermal and pH stability at various conditions that mimic milk manufacturing and supply chain conditions. It also demonstrated a significant reduction in Salmonella concentration in media at various MOIs, with higher bacterial eradication at higher MOI. Moreover, it significantly reduced Salmonella growth (MOI 1) in milk, manifesting a 1000-fold decrease in bacteria concentration following 3 h incubation at 37 °C. The results highlighted the strong ability of ZCSE6 to kill Salmonella and control its growth in milk. Thus, ZCSE6 is recommended as a biocontrol agent in milk to limit bacterial growth and increase the milk shelf-life.

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A New Sahidic Fragment of the Gospel of Luke from the Michigan Collection

Novum Testamentum ◽

10.1163/15685365-12341434 ◽

2014 ◽

Vol 56 (2) ◽

pp. 198-204

Author(s):

Brice C. Jones

Keyword(s):

Gospel Of Luke ◽

Almost All ◽

First Time

AbstractThis article publishes for the first time the extant remains of a Sahidic Coptic manuscript containing portions of Luke 17-19. Almost all of the special Lukan pericope concerning Jesus and Zacchaeus is preserved (19:1-10), as well as most of the parable of the Dishonest Judge (18:1-8). The edition includes a transcription, translation, palaeographical analysis, critical apparatus, as well as images of the fragment.

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Descriptive and illustrated diagnosis of Ophiuroidea fauna (Echinodermata) in the shallow waters of North-eastern Brazil

Marine Biodiversity Records ◽

10.1017/s1755267215000652 ◽

2015 ◽

Vol 8 ◽

Author(s):

Fabilene Gomes Paim ◽

Maria Cecília Guerrazzi ◽

Michela Borges

Keyword(s):

Brittle Star ◽

Shallow Waters ◽

Bottom Substrate ◽

Eastern Brazil ◽

North Eastern ◽

Amphipholis Squamata ◽

Biological Substrates ◽

Almost All ◽

First Time ◽

Ophiocoma Echinata

In this study, we present descriptions, illustrations, comments, and bathymetric and geographic distributions of the brittle star species related to the estuary region of Camamu Bay, located in the State of Bahia, Brazil. The brittle star fauna lives on biological substrates, sand bottoms, mud and rubble in the Camamu Bay and comprises 12 species divided into five families. Almost all of them are common in the tropical and subtropical fauna of the regions of shallow water.Ophiophragmus filograneusis reported for the first time in Bahia, and nine other species are recorded for the first time in Camamu Bay:Amphipholis januarii, Amphipholis squamata, Ophiophragmus filograneus, Ophiostigma isocanthum,Ophioderma cinerea, Ophioderma januarii, Ophiactis lymani, Ophiactis savignyi andOphiocoma echinata.The results suggest that the ophiuroid assemblages are strongly affected by marine currents as well as by different kinds of bottom substrate.

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P009 Disease classifier and microbial dysbiosis index tools cross-predict various pathogenic conditions due to general microbial signal

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab076.138 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S129-S129

Author(s):

H Abbas Egbariya ◽

T Braun ◽

R Hadar ◽

O Gal-Mor ◽

N Shental ◽

...

Keyword(s):

Random Forest ◽

Disease Control ◽

Control Cohort ◽

Sequencing Data ◽

Microbial Dysbiosis ◽

Trained Classifier ◽

The Status ◽

Inflammatory Bowel ◽

General Response ◽

Log Ratio

Abstract Background Microbial dysbiosis is widely described in inflammatory bowel disease (IBD), and has been shown to predict IBD state. However, many other diseases including neuro-psychiatric, metabolic, and malignancies, most of which do not result in gut inflammation, are also linked with gut microbial alteration. Since most studies focus on a single disease, the extent of similarity between different diseases is usually not examined. Methods We reanalyzed raw sequencing data from 12,838 human gut V4 16Sseq samples, spanning 59 case-controls comparisons and 28 unique diseases. Novel statistical approach was applied to reduce the effect of the different cohorts; all samples were processed uniformly, and differentially expressed amplicon sequence variants (ASVs) were identified within each cohort. The resulting behavior (direction of change and effect size) of each ASV were then combined across all studies. We used random forest as our classifier and generated non-specific dysbiosis index (NSDI). Results For the disease prediction, each cohort was randomly subsampled to 23 healthy and 23 disease samples. Random forest classifier was trained on one disease/control cohort, and the trained classifier was then used to predict the status of a different disease/control cohort. Disease classifiers performed well in identifying many sick vs. healthy states but failed to differentiate between different diseases. For example, a classifier trained on IBD cohort classified relatively good also disease/control in lupus, schizophrenia, or Parkinson’s from different cohorts. We show this cross-identification is due to a large number of shared disease-associated bacteria and utilize these bacteria to define a novel non-specific dysbiosis index (NSDI). After, we identified 114 non-disease specific ASVs (86 up and 28 down regulated ASVs across diseases in comparison to controls), we calculate the per-sample NSDI by rank-transforming the bacteria within the sample and computing the normalized log ratio of the sum of the ranks of the 86 down and 28 up regulated ASVs. The resulting NSDI is shown to perform better than the previously published CD dysbiosis index (Gevers et al, 2014; PMID: 24629344) indicating that NSDI can successfully differentiate between most cases and controls across a wide variety of diseases. Conclusion A robust non-specific general response of the gut microbiome is detected across different diseases, some of which is shared with IBD. Classifiers trained on a single disease may identify the general non-specific signal and therefore care should be taken when interpreting the classifier predictions. Finally, our NSDI can be used to prioritize the per-sample degree of dysbiosis.

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The Diversity of Bacteria Associated with the Invasive Gall Wasp Dryocosmus kuriphilus, Its Galls and a Specialist Parasitoid on Chestnuts

Insects ◽

10.3390/insects13010086 ◽

2022 ◽

Vol 13 (1) ◽

pp. 86

Author(s):

Xiaohui Yang ◽

Yu Hui ◽

Daohong Zhu ◽

Yang Zeng ◽

Lvquan Zhao ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Plant Pathogens ◽

High Throughput Sequencing ◽

Bacterial Species ◽

Gall Wasp ◽

Potential Vector ◽

Dryocosmus Kuriphilus ◽

Torymus Sinensis ◽

Galling Insects ◽

First Time

Dryocosmus kuriphilus (Hymenoptera: Cynipidae) induces galls on chestnut trees, which results in massive yield losses worldwide. Torymus sinensis (Hymenoptera: Torymidae) is a host-specific parasitoid that phenologically synchronizes with D. kuriphilus. Bacteria play important roles in the life cycle of galling insects. The aim of this research is to investigate the bacterial communities and predominant bacteria of D. kuriphilus, T. sinensis, D. kuriphilus galls and the galled twigs of Castanea mollissima. We sequenced the V5–V7 region of the bacterial 16S ribosomal RNA in D. kuriphilus, T. sinensis, D. kuriphilus galls and galled twigs using high-throughput sequencing for the first time. We provide the first evidence that D. kuriphilus shares most bacterial species with T. sinensis, D. kuriphilus galls and galled twigs. The predominant bacteria of D. kuriphilus are Serratia sp. and Pseudomonas sp. Furthermore, the bacterial community structures of D. kuriphilus and T. sinensis clearly differ from those of the other groups. Many species of the Serratia and Pseudomonas genera are plant pathogenic bacteria, and we suggest that D. kuriphilus may be a potential vector of plant pathogens. Furthermore, a total of 111 bacteria are common to D. kuriphilus adults, T. sinensis, D. kuriphilus galls and galled twigs, and we suggest that the bacteria may transmit horizontally among D. kuriphilus, T. sinensis, D. kuriphilus galls and galled twigs on the basis of their ecological associations.

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A unified haplotype-based method for accurate and comprehensive variant calling

10.1101/456103 ◽

2018 ◽

Cited By ~ 3

Author(s):

Daniel P Cooke ◽

David C Wedge ◽

Gerton Lunter

Keyword(s):

De Novo ◽

Variant Calling ◽

Normal Sample ◽

Sequencing Data ◽

Somatic Variation ◽

Data Set ◽

Small Complex ◽

Physical Linkage ◽

Germline Variation ◽

Almost All

Haplotype-based variant callers, which consider physical linkage between variant sites, are currently among the best tools for germline variation discovery and genotyping from short-read sequencing data. However, almost all such tools were designed specifically for detecting common germline variation in diploid populations, and give sub-optimal results in other scenarios. Here we present Octopus, a versatile haplotype-based variant caller that uses a polymorphic Bayesian genotyping model capable of modeling sequencing data from a range of experimental designs within a unified haplotype-aware framework. We show that Octopus accurately calls de novo mutations in parent-offspring trios and germline variants in individuals, including SNVs, indels, and small complex replacements such as microinversions. In addition, using a carefully designed synthetic-tumour data set derived from clean sequencing data from a sample with known germline haplotypes, and observed mutations in large cohort of tumour samples, we show that Octopus accurately characterizes germline and somatic variation in tumours, both with and without a paired normal sample. Sequencing reads and prior information are combined to phase called genotypes of arbitrary ploidy, including those with somatic mutations. Octopus also outputs realigned evidence BAMs to aid validation and interpretation.

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Exactly separable version of the Bohr Hamiltonian with the Davidson potential

HNPS Proceedings ◽

10.12681/hnps.2589 ◽

2020 ◽

Vol 16 ◽

pp. 121

Author(s):

D. Bonatsos ◽

E. A. McCutchan ◽

N. Minkov ◽

R. F. Casten ◽

P. Yotov ◽

...

Keyword(s):

Dynamical Symmetry ◽

Transition Rates ◽

Stiffness Parameter ◽

Oscillator Potential ◽

Harmonic Oscillator Potential ◽

Boson Model ◽

Two Parameters ◽

Almost All ◽

First Time ◽

Davidson Potential

An exactly separable version of the Bohr Hamiltonian, is obtained by using a potential of the form V (β, γ) = u(β) + u(γ)/β2, with a Davidson potential for u(β) and a stiff harmonic oscillator potential centered around γ = 0o, for u(γ).Using two parameters (β0 and the γ-stiffness parameter) the band features and B(E2) transition rates of almost all well-deformed rare-earth and actinide nuclei are reproduced, while the spectrum of the SU(3) dynamical symmetry of the Interacting Boson Model can be obtained, for the first time using the Bohr Hamiltonian.

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