scholarly journals Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis

Microbiology ◽  
2009 ◽  
Vol 155 (4) ◽  
pp. 1103-1110 ◽  
Author(s):  
Gundula Bosch ◽  
Tiansong Wang ◽  
Ekaterina Latypova ◽  
Marina G. Kalyuzhnaya ◽  
Murray Hackett ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Profile ◽  
Shotgun Proteomics ◽  
Metagenomic Sequencing ◽  
Sequence Coverage ◽  
Metagenomic Sequence ◽  
The Family ◽  
Proteomics Approach ◽  
Sequence Quality ◽  
Environmental Microbes

While the shotgun proteomics approach is gaining momentum in understanding microbial physiology, it remains limited by the paucity of high-quality genomic data, especially when it comes to poorly characterized newly identified phyla. At the same time, large-scale metagenomic sequencing projects produce datasets representing genomes of a variety of environmental microbes, although with lower sequence coverage and sequence quality. In this work we tested the utility of a metagenomic dataset enriched in sequences of environmental strains of Methylotenera mobilis, to assess the protein profile of a laboratory-cultivated strain, M. mobilis JLW8, as a proof of principle. We demonstrate that a large portion of the proteome predicted from the metagenomic sequence (approx. 20 %) could be identified with high confidence (three or more peptide sequences), thus gaining insights into the physiology of this bacterium, which represents a new genus within the family Methylophilaceae.

A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

1996 ◽  
Vol 5 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Chris Halpin ◽  
Barbara Herrmann ◽  
Margaret Whearty
Keyword(s):  
Speech Production ◽  
Hearing Aids ◽  
Role Models ◽  
Speech Intelligibility ◽  
Large Scale ◽  
Speech Language Pathology ◽  
The Family ◽  
Patient Will ◽  
Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

The Use of Medical Record Linkage for Population and Genetic Studies

1969 ◽  
Vol 08 (01) ◽  
pp. 07-11 ◽  
Author(s):  
H. B. Newcombe
Keyword(s):  
Record Linkage ◽  
Large Scale ◽  
Medical Record Linkage ◽  
Canadian Province ◽  
Genetic Studies ◽  
Parental Characteristics ◽  
Family Histories ◽  
The Family ◽  
Large Populations ◽  
Machine Readable

Methods are described for deriving personal and family histories of birth, marriage, procreation, ill health and death, for large populations, from existing civil registrations of vital events and the routine records of ill health. Computers have been used to group together and »link« the separately derived records pertaining to successive events in the lives of the same individuals and families, rapidly and on a large scale. Most of the records employed are already available as machine readable punchcards and magnetic tapes, for statistical and administrative purposes, and only minor modifications have been made to the manner in which these are produced.As applied to the population of the Canadian province of British Columbia (currently about 2 million people) these methods have already yielded substantial information on the risks of disease: a) in the population, b) in relation to various parental characteristics, and c) as correlated with previous occurrences in the family histories.

Circulating microbial cell-free DNA is associated with inflammatory host-responses in severe pneumonia

Thorax ◽  
2021 ◽  
pp. thoraxjnl-2020-216013
Author(s):  
Haopu Yang ◽  
Ghady Haidar ◽  
Nameer S Al-Yousif ◽  
Haris Zia ◽  
Daniel Kotok ◽  
...  
Keyword(s):  
Large Scale ◽  
Inflammatory Responses ◽  
Severe Pneumonia ◽  
Systemic Circulation ◽  
Microbial Cell ◽  
Metagenomic Sequencing ◽  
Cell Free Dna ◽  
Free Dna ◽  
Culture Positive ◽  
Culture Negative

Host inflammatory responses predict worse outcome in severe pneumonia, yet little is known about what drives dysregulated inflammation. We performed metagenomic sequencing of microbial cell-free DNA (mcfDNA) in 83 mechanically ventilated patients (26 culture-positive, 41 culture-negative pneumonia, 16 uninfected controls). Culture-positive patients had higher levels of mcfDNA than those with culture-negative pneumonia and uninfected controls (p<0.005). Plasma levels of inflammatory biomarkers (fractalkine, procalcitonin, pentraxin-3 and suppression of tumorigenicity-2) were independently associated with mcfDNA levels (adjusted p<0.05) among all patients with pneumonia. Such host–microbe interactions in the systemic circulation of patients with severe pneumonia warrant further large-scale clinical and mechanistic investigations.

scholarly journals MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 726
Author(s):  
Mike W.C. Thang ◽  
Xin-Yi Chua ◽  
Gareth Price ◽  
Dominique Gorse ◽  
Matt A. Field
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Differential Analysis ◽  
Biomedical Sciences ◽  
Metagenomic Sequence ◽  
Differential Abundance ◽  
Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences.  While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs.  Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics.  MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

scholarly journals An assessment of the population status of the threatened medicinal plant Illicium griffithii Hook.f. & Thomson in West Kameng District of Arunachal Pradesh, India

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Tashi Dorjee Bapu ◽  
Gibji Nimasow
Keyword(s):  
Medicinal Plant ◽  
Large Scale ◽  
Arunachal Pradesh ◽  
Mature Trees ◽  
Regeneration Rate ◽  
Dead Trees ◽  
Threatened Medicinal Plant ◽  
The Family ◽  
Proper Training ◽  
Large Scale Cultivation

Illicium griffithii Hook.f. & Thomson, a medicinal plant of the family Schisandraceae, is an Endangered species listed by the IUCN.  A decline in population of this plant due to climate change as well as increasing human influences on the natural resources has been a matter of great concern among the researchers.  In order to estimate the existing population of this plant, a field-based study employing linear transect method was conducted in four phases, May–June 2017, May–June 2018, April–May 2019, October–November 2019 covering an area of 700km² (approx.) in West Kameng District of Arunachal Pradesh that lies within the Himalayan biodiversity hotspot.  The study recorded 3,044 live individuals of I. griffithii including 1,372 seedlings, 1,358 saplings, and only 314 mature trees.  Additionally, 126 dead trees were also recorded.  The study confirmed that the plant has a good regeneration rate but with a poor survival rate of saplings.  Besides, large-scale collection of its fruits for trade and anthropogenic disturbances in the study area appears to be the major threat to its existing population.  Therefore, proper training of the local people on large-scale cultivation of this plant together with awareness towards judicious harvesting of fruits from the wild may be the significant approach to conservation. 

scholarly journals Online parallel accumulation − serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

2018 ◽  
Author(s):  
Florian Meier ◽  
Andreas-David Brunner ◽  
Scarlet Koch ◽  
Heiner Koch ◽  
Markus Lubeck ◽  
...  
Keyword(s):  
Cross Sections ◽  
Ion Mobility ◽  
Large Scale ◽  
High Efficiency ◽  
Low Voltage ◽  
Shotgun Proteomics ◽  
Trapped Ion ◽  
Operating Modes ◽  
Third Dimension ◽  
Mobility Device

ABSTRACTIn bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-fight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive due to its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation – serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 800,000 fragmentation spectra in standard 120 min LC runs are easily achievable, which can be used for near exhaustive precursor selection in complex mixtures or re-sequencing weak precursors. MaxQuant identified more than 6,400 proteins in single run HeLa analyses without matching to a library, and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,900 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.

scholarly journals DNA screening of Drosophila suzukii predators in berry field orchards shows new predatory taxonomical groups

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249673
Author(s):  
Sara Sario ◽  
Conceição Santos ◽  
Fátima Gonçalves ◽  
Laura Torres
Keyword(s):  
Large Scale ◽  
Field Studies ◽  
Life Cycles ◽  
Gut Content ◽  
Drosophila Suzukii ◽  
Potential Predator ◽  
The Family ◽  
First Time ◽  
South Europe ◽  
New Habitats

Drosophila suzukii (spotted wing drosophila, SWD) is a pandemic quarantine pest that attacks mostly red fruits. The high number of life cycles per year, its ability to rapidly invade and spread across new habitats, and highly polyphagous nature, makes this a particularly aggressive invasive species, for which efficient control methods are currently lacking. The use of native natural predators is particularly promising to anchor sustainable and efficient measures to control SWD. While several field studies have suggested the presence of potential predatory species in infested orchards, only a few confirmed the presence of SWD DNA in predators’ gut content. Here, we use a DNA-based approach to identify SWD predators among the arthropod diversity in South Europe, by examining the gut content of potential predator specimens collected in SWD-infested berry fields in North Portugal. These specimens were morphologically identified to the family/order, and their gut content was screened for the presence of SWD DNA using PCR. New SWD predatory taxonomical groups were identified, as Opiliones and Hemerobiidae, in addition to known SWD predators, such as Hemerobiidae, Chrysopidae, Miridae, Carabidae, Formicidae and Araneae. Additionally, the presence of a spider family, Uloboridae, in the orchards was recorded for the first time, posing this family as another SWD-candidate predator. This study sets important bases to further investigate the potential large-scale use of some of these confirmed predator taxa for SWD control in South Europe.

scholarly journals New insights into Trypanosoma cruzi evolution and genotyping based on system-wide protein expression profiles (PhyloQuant)

2020 ◽  
Author(s):  
Simon Ngao Mule ◽  
Andrè Guillherme da Costa Martins ◽  
Livia Rosa-Fernandes ◽  
Gilberto Santos de Oliveira ◽  
Carla Monadeli Rodrigues ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Trypanosoma Cruzi ◽  
Protein Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Shotgun Proteomics ◽  
Close Correlation ◽  
Evolutionary Relationships ◽  
Trypanosome Species ◽  
Protein Expression Profiles

AbstractThe etiological agent of Chagas disease, Trypanosoma cruzi, is subdivided into seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution justifies the concerted efforts towards understanding the population structure of T. cruzi strains. In this study, we introduce a novel approach termed ‘phyloquant’ to infer the evolutionary relationships and assignment of T. cruzi strains to their DTUs based on differential protein expression profiles evidenced by bottom up large scale mass spectrometry-based quantitative proteomic features. Mass spectrometry features analyzed using parsimony (MS1, iBAQ and LFQ) showed a close correlation between protein expression and T. cruzi DTUs and closely related trypanosome species. Although alternative topologies with minor differences between the three MS features analyzed were demonstrated, we show congruence to well accepted evolutionary relationships of T. cruzi DTUs; in all analyses TcI and Tcbat were sister groups, and the parental nature of genotype TcII and the hybrid genotypes TcV/TcVI were corroborated. Character mapping of genetic distance matrices based on phylogenetics and phyloquant clustering showed statistically significant correlations. We propose the first quantitative shotgun proteomics approach as a complement strategy to the genetic-based assignment of T. cruzi strains to DTUs and evolutionary inferences. Moreover, this approach allows for the identification of differentially regulated and strain/DTU/species-specific proteins, with potential application in the identification of strain/DTU specific biomarkers and candidate therapeutic targets. In addition, the correlation between multi-gene protein expression and divergence of trypanosome species was evaluated, adding another level to understand the genetic subdivisions among T. cruzi DTUs.

scholarly journals Elucidating the Function of an Ancient NF-κB p100 Homologue, CrRelish, in Antibacterial Defense

2007 ◽  
Vol 76 (2) ◽  
pp. 664-670 ◽  
Author(s):  
Ze Hua Fan ◽  
Xiao Wei Wang ◽  
Jinhua Lu ◽  
Bow Ho ◽  
Jeak Ling Ding
Keyword(s):  
Time Course ◽  
Horseshoe Crab ◽  
Secondary Infection ◽  
Protein Profile ◽  
Sequence Context ◽  
Living Fossil ◽  
Immune Priming ◽  
Repeated Infection ◽  
The Family

ABSTRACT The family of NF-κB transcription factors essentially regulates immune-related gene expression. Recently, we isolated and characterized the classical NF-κB/inhibitor κB (IκB) homologues from a “living fossil,” the horseshoe crab, Carcinoscorpius rotundicauda. Interestingly, this ancient species also harbors another class I NF-κB p100 homologue, C. rotundicauda Relish (CrRelish). Similar to Drosophila Relish and the mammalian p100, CrRelish contains both the Rel-homology domains (RHD) and the IκB-like domain. In this study, we found that the RHD of CrRelish can recognize horseshoe crab and human κB response elements and activate the downstream reporter in vitro, thereby suggesting the evolutionary conservation of this molecule. Pseudomonas aeruginosa infection transcriptionally upregulates CrRelish, which exhibits a dynamic protein profile over the time course of infection. Surprisingly, secondary infection reinduced an upsurge in CrRelish protein expression to a level which overrode the protein degradation at 12 h postinfection. These observations strongly suggest the involvement of CrRelish in antibacterial defense. Secondary infection causes (i) the maintenance of a favorable expression-competent sequence context of the CrRelish gene and/or (ii) the derepression or stabilization of the CrRelish transcript resulting from the primary infection to enable the more rapid expression and accumulation of the CrRelish protein, reflecting apparent signal/immune priming in a repeated infection.

Conflict of laws regulation of the international family relations in the Russian Federation (legislation and jurisprudence)

2021 ◽  
pp. 127
Author(s):  
Irina Get’man-Pavlova
Keyword(s):  
Russian Federation ◽  
Large Scale ◽  
Family Relations ◽  
Private International Law ◽  
Legal Doctrine ◽  
Marriage And Family ◽  
Conflict Of Laws ◽  
The Family ◽  
The Russian Federation ◽  
The Law

Russian conflict of laws rules that determine the choice of law applicable to marriage and family relations associated with foreign law and order came into force in 1995 and have been in effect for more than 25 years. Despite the fact that this problem has been studied in great detail in the Russian legal doctrine, the relevance of the analysis of conflict of laws rules set forth in the Family Code of the Russian Federation is by no means exhausted due to the large-scale reform of the rules of Private International Law in the Civil Code of the Russian Federation and the current legislative regulation of international family relations in other States. The article concludes that conflict of laws regulation of the international family relations in the Russian Federation adopted more than 25 years ago needs serious modernization. It is reasonable to carry out the corresponding updating in the following directions: maximum specification of the content of conflict of laws rules for the purpose of more differentiated regulation of the family relations; establishment of a complex and detailed system of the connecting factors aimed at correct determination of the law the most closely connected with the relation and decision-making; the expansion of possibility of choice of the applicable law to divorce and property relations; application of the law the most favorable for a child should become a dominating connecting factor.

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