scholarly journals Growth by Insertion: The Family of Bacterial DDxP Proteins

2020 ◽  
Vol 21 (23) ◽  
pp. 9184
Author(s):  
Pierpaolo Di Nocera ◽  
Eliana De Gregorio
Keyword(s):  
Amino Acids ◽  
Target Site ◽  
Homologous Proteins ◽  
The Family ◽  
Different Types ◽  
Genes Encoding ◽  
Multiple Copies

We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp–Asp–x–Pro (DDxP) motifs. DDxP proteins range in size from 900 to 6200 aa (amino acids), and contain 1 to 5 different module types, present in one or multiple copies. We hypothesize that DDxP proteins were modeled by the action of specific endonucleases inserting DNA segments into genes encoding DDxP motifs. Target site duplications (TSDs) formed upon repair of staggered ends generated by endonuclease cleavage would explain the DDxP motifs at repeat ends. TSDs acted eventually as targets for the insertion of more modules of the same or different types. Repeat clusters plausibly resulted from amplification of both repeat and flanking TSDs. The proposed growth shown by the insertion model is supported by the identification of homologous proteins lacking repeats in Pseudomonas and Rhizobium. The 85 DDxP repeats identified in this work vary in length, and can be sorted into short (136–215 aa) and long (243–304 aa) types. Conserved Asp–Gly–Asp–Gly–Asp motifs are located 11–19 aa from the terminal DDxP motifs in all repeats, and far upstream in most long repeats.

scholarly journals Degenerative Minimalism in the Genome of a Psyllid Endosymbiont

2001 ◽  
Vol 183 (6) ◽  
pp. 1853-1861 ◽  
Author(s):  
Marta A. Clark ◽  
Linda Baumann ◽  
MyLo Ly Thao ◽  
Nancy A. Moran ◽  
Paul Baumann
Keyword(s):  
Amino Acids ◽  
Extreme Case ◽  
Amino Acid Sequences ◽  
Compositional Bias ◽  
Buchnera Aphidicola ◽  
Homologous Proteins ◽  
Protein Coding ◽  
Phloem Sap ◽  
Promoter Sequences ◽  
Genes Encoding

ABSTRACT Psyllids, like aphids, feed on plant phloem sap and are obligately associated with prokaryotic endosymbionts acquired through vertical transmission from an ancestral infection. We have sequenced 37 kb of DNA of the genome of Carsonella ruddii, the endosymbiont of psyllids, and found that it has a number of unusual properties revealing a more extreme case of degeneration than was previously reported from studies of eubacterial genomes, including that of the aphid endosymbiont Buchnera aphidicola. Among the unusual properties are an exceptionally low guanine-plus-cytosine content (19.9%), almost complete absence of intergenic spaces, operon fusion, and lack of the usual promoter sequences upstream of 16S rDNA. These features suggest the synthesis of long mRNAs and translational coupling. The most extreme instances of base compositional bias occur in the genes encoding proteins that have less highly conserved amino acid sequences; the guanine-plus-cytosine content of some protein-coding sequences is as low as 10%. The shift in base composition has a large effect on proteins: in polypeptides of C. ruddii, half of the residues consist of five amino acids with codons low in guanine plus cytosine. Furthermore, the proteins ofC. ruddii are reduced in size, with an average of about 9% fewer amino acids than in homologous proteins of related bacteria. These observations suggest that the C. ruddii genome is not subject to constraints that limit the evolution of other known eubacteria.

Methionine-Specific Staining of Collagen

1982 ◽  
Vol 40 ◽  
pp. 294-295
Author(s):  
E.M. Kuhn ◽  
K.D. Marenus ◽  
M. Beer
Keyword(s):  
Amino Acids ◽  
Collagen Fibers ◽  
Type Iii Collagen ◽  
Type I ◽  
Electron Microscopic ◽  
Good Correspondence ◽  
Specific Staining ◽  
Type Iii ◽  
Different Types ◽  
Sulfur Containing

Fibers composed of different types of collagen cannot be differentiated by conventional electron microscopic stains. We are developing staining procedures aimed at identifying collagen fibers of different types.Pt(Gly-L-Met)Cl binds specifically to sulfur-containing amino acids. Different collagens have methionine (met) residues at somewhat different positions. A good correspondence has been reported between known met positions and Pt(GLM) bands in rat Type I SLS (collagen aggregates in which molecules lie adjacent to each other in exact register). We have confirmed this relationship in Type III collagen SLS (Fig. 1).

The Arabic Origins of English and Indo-European “Definite Articles”: A Radical Linguistic Theory Approach

2016 ◽  
Vol 4 (6) ◽  
pp. 26
Author(s):  
Zaidan Ali Jassem
Keyword(s):  
Comparative Method ◽  
Linguistic Theory ◽  
General Level ◽  
Theory Approach ◽  
Tree Model ◽  
Linguistic Change ◽  
European Languages ◽  
The Family ◽  
Different Types ◽  
Definite Articles

This paper traces the Arabic origins or cognates of the “definite articles” in English and Indo-European languages from a radical linguistic (or lexical root) theory perspective. The data comprises the definite articles in English, German, French, Spanish, Portuguese, Italian, Romanian, Latin, Greek, Macedonian, Russian, Polish, Sanskrit, Hindi, Bengali, Persian, and Arabic. The results clearly indicate that five different types of such articles emerged in the data, all of which have true Arabic cognates with the same or similar forms and meanings, whose differences are due to natural and plausible causes and different routes of linguistic change, especially lexical, semantic, or morphological shift. Therefore, the results support the adequacy of the radical linguistic theory according to which, unlike the Family Tree Model or Comparative Method, Arabic, English, German, French, Latin, Greek, and Sanskrit not only belong to the same language family, renamed Eurabian or Urban family, but also are dialects of the same language, with Arabic being their origin all because only it shares the whole cognates with them all and because it has a huge phonetic, morphological, grammatical, and lexical variety. They also manifest fundamental flaws and grave drawbacks which plague English and Indo-European lexicography for ignoring Arabic as an ultimate ancestor and progenitor not only in the treatment of the topic at hand but in all others in general. On a more general level, they also show that there is a radical language from which all human languages stemmed and which has been preserved almost intact in Arabic, thus being the most conservative and productive language

scholarly journals Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
He-Teng Zhang ◽  
Hao Wang ◽  
Hai-Sheng Wu ◽  
Jian Zeng ◽  
Yan Yang
Keyword(s):  
Human Papillomavirus ◽  
Bacterial Community ◽  
Pregnant Women ◽  
Sequence Comparison ◽  
Pairwise Sequence Comparison ◽  
Vaginal Secretion ◽  
The Family ◽  
Complete Genomes ◽  
Different Types ◽  
Vaginal Tract

Abstract Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

scholarly journals Suitability of sugar, amino acid, and inorganic ion compositions to distinguish fir and spruce honey

2021 ◽  
Author(s):  
Basel Shaaban ◽  
Victoria Seeburger ◽  
Annette Schroeder ◽  
Gertrud Lohaus
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Picea Abies ◽  
Multivariate Analyses ◽  
Abies Alba ◽  
Inorganic Ions ◽  
Scale Insects ◽  
Inorganic Ion ◽  
Plant Feeding ◽  
Different Types

AbstractHoneydew honey is produced by bees from excretions of plant-feeding insects, such as aphids and scale insects. Honeydew on conifers, like fir (Abies alba) or spruce (Picea abies), is produced by different species of the genera Cinara and Physokermes. This means that honeydew honey can stem from different botanical as well as zoological origins, but so far it is not possible to clearly distinguish the different types of honeys. In the attempt to identify distinguishing markers, 19 sugars, 25 amino acids and 9 inorganic ions were quantified in three groups of honeydew honey (fir/Cinara, spruce/Cinara and spruce/Physokermes) with 20 honey samples each. It could be demonstrated that the contents of isomaltose, raffinose, erlose, two undefined oligosaccharides, several amino acids, sulfate, and phosphate differed significantly between the three groups of honey. Furthermore, multivariate analyses resulted in a separation of spruce/Physokermes honey from spruce- or fir/Cinara honey due to its higher contents of phosphate, sulfate, erlose and two undefined oligosaccharides. Moreover, the amino acid composition and the isomaltose as well as the raffinose contents proved useful in the distinction between fir/Cinara and spruce/Cinara honey. In sum, the contents of sugars, amino acids, and inorganic ions in German fir and spruce honeys provide useful information about the botanical and zoological origin of honeydew honeys.

A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 613-621 ◽  
Author(s):  
Douglas R Dorer ◽  
Jamie A Rudnick ◽  
Etsuko N Moriyama ◽  
Alan C Christensen
Keyword(s):  
Phylogenetic Analysis ◽  
Drosophila Melanogaster ◽  
Anopheles Gambiae ◽  
Evolutionary History ◽  
Codon Bias ◽  
Good Target ◽  
The Family ◽  
Genes Encoding ◽  
And Function ◽  
Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

scholarly journals 431 - DEMENTIA IN PRIMARY CARE AND DOCTOR-PATIENT-CARER INTERACTIONS: PRELIMINARY FINDINGS

2020 ◽  
Vol 32 (S1) ◽  
pp. 147-147
Author(s):  
Conceição Balsinha ◽  
Steve Iliffe ◽  
Sónia Dias ◽  
Manuel Gonçalves-Pereira
Keyword(s):  
Primary Care ◽  
Family Carer ◽  
Family Carers ◽  
Medical Encounter ◽  
Triadic Interactions ◽  
Patient Interactions ◽  
The Family ◽  
Different Types ◽  
Third Person ◽  
Ongoing Project

INTRODUCTION: Primary care visits of persons with dementia involve different types of communication, bringing together the patient, the family carer and the general practitioner (GP). A particular challenge is the necessary involvement of a third person (the carer) in patient-doctor encounters (or the patient in carer-doctor encounters, as dementia advances). These triad dynamics should be better understood, as health outcomes are expected to result from or be mediated by them.OBJECTIVE: Our aim is to explore triadic dynamics in Portuguese primary care consultations with persons with dementia, their family carers and GPs.METHODS: This is the first part of an ongoing project (Dementia in Primary Care: the Patient, the Carer and the Doctor in the Medical Encounter - Bayer Investigation Grant | NOVAsaúde Ageing 2018). Consultations with persons with dementia, their carers and GPs (purposive sampling) are audio-recorded, transcribed verbatim and thematically analysed. We report the analysis of interactions of the first six consultations, using NVIVO® software.RESULTS: The most frequent type of interaction was between GPs and carers, followed by interactions involving the whole triad. The patients who had more recent relationships with their GPs tended to participate less, irrespective of the stage of dementia. Carers were the ones most often initiating triadic interactions, and GPs the ones most often terminating them by directly addressing the patients. Doctor-carers interactions were very sparse in some consultations.DISCUSSION AND CONCLUSION: These preliminary findings suggest that doctor-patient interactions may be limited in a number of GPs’ consultations, seemingly compromising patient-centred approaches. Nevertheless, even when GPs were involved in triadic interactions they often tried to address the patient directly. We are looking forward to complete this part of the project: to our knowledge, there is practically no evidence from live-recorded primary care consultations about these triadic dynamics.

Disability in Schizophrenic Disorders

2009 ◽  
Vol 24 (S1) ◽  
pp. 1-1
Author(s):  
J. Wancata ◽  
M. Freidl ◽  
F. Friedrich ◽  
T. Matschnig ◽  
A. Unger ◽  
...  
Keyword(s):  
Hospital Admissions ◽  
Social Consequences ◽  
Subjective Burden ◽  
Social Contacts ◽  
Mothers And Fathers ◽  
Duration Of Illness ◽  
The Family ◽  
Different Types ◽  
Icd 10 ◽  
The Mean

Aims:The purpose of this study was to investigate disability among patients suffering from schizophrenia and to identify predictors of disability.Methods:101 patients from different types of psychiatric services in Vienna and diagnosed with schizophrenia according to ICD-10 were included. They were investigates by means of 36-Item self-administered version of the WHO Disability Assessment Schedule II (WHO-DAS-II) and the PANSS-scale. Patients’ mothers and fathers were asked to fill in the Family Problem Questionnaire.Results:The mean total score of the WHO-DAS-II was 74.1 (SD 21.9). When using weighted sub-scores the highest disability scores were found for social contacts, participation in society and household (means 2.58, 2.57 and 2.51 respectively). Using logistic regression, overall disability was positively associated with patient's age, overall severity of symptoms (PANSS) and number of previous hospital admissions. Overall disability was not associated with duration of illness and or patient's gender. The subjective burden experienced by patients’ fathers and mothers were increased by reduced social contacts and impaired participation in society, while we could not find an association with other domains of patient's disability (understanding, mobility, self-care, household).Conclusions:This study shows that schizophrenia results in disability in several domains. Family caregivers’ burden was predominantly increased by social consequences of schizophrenia.

scholarly journals Characterization of porcine osteonectin extracted from foetal calvariae

1988 ◽  
Vol 253 (1) ◽  
pp. 139-151 ◽  
Author(s):  
C Domenicucci ◽  
H A Goldberg ◽  
T Hofmann ◽  
D Isenman ◽  
S Wasi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Type I Collagen ◽  
Culture Shock ◽  
Gel Filtration ◽  
Alpha Helix ◽  
Type I ◽  
Homologous Proteins ◽  
Compact Structure ◽  
Significant Difference

Osteonectin, extracted from foetal porcine calvariae with 0.5 M-EDTA, was purified to homogeneity by using gel filtration and polyanion anion-exchange fast protein liquid chromatography under dissociative conditions without the need of reducing agents. The purified protein migrated with an Mr of 40,300 on SDS/polyacrylamide gels and was similar to bovine osteonectin in both amino acid composition and in its ability to bind to hydroxyapatite in the presence of 4 M-guanidinium hydrochloride (GdmCl). However, unlike the bovine protein, porcine osteonectin did not bind selectively to hydroxyapatite when EDTA tissue extracts were used. In addition, purified porcine osteonectin did not show any apparent affinity for either native or denatured type I collagen, but did bind to serum albumin. Primary sequence analysis revealed an N-terminal alanine residue, with approximately one-half of the subsequent 35 residues identified as small hydrophobic amino acids and one-quarter as acidic amino acids. The only significant difference between the N-terminal sequences of the bovine and porcine proteins was the deletion of the tripeptide Val-Ala-Glu in porcine osteonectin. In contrast with bovine osteonectin, far-u.v.c.d. of porcine osteonectin revealed considerable secondary structure, of which 27% was alpha-helix and 39% was beta-sheet. Cleavage of the molecule with CNBr under non-reducing conditions generated five fragments, of which two major fragments (Mr 27,900 and 12,400) stained blue with Stains All, a reagent that stains sialic-acid-rich proteins/phosphate-containing proteins and/or Ca2+-binding proteins blue while staining other proteins pink. The 12,400-Mr fragment bound 45Ca2+ selectively, indicating a Ca2+-binding site in this part of the molecule. The 27,900-Mr fragment did not bind Ca2+, and since biosynthetic studies with 32PO4(3-) did not show phosphorylation of porcine osteonectin, this fragment is likely to be highly acidic. The incomplete cleavage of the molecule with CNBr and the ability of the molecule to regain its secondary structure after exposure to 7 M-urea are features consistent with the molecule having a compact structure that is stabilized by numerous disulphide bridges. The chemical and binding properties of porcine osteonectin are closely similar to the recently described ‘culture shock’, SPARC and BM-40 proteins, indicating that these are homologous proteins.

scholarly journals “A dismantled society”: meta-synthesis of the phenomenon of violence in indigenous populations

2018 ◽  
Vol 39 (0) ◽  
Author(s):  
Berenice Juan-Martínez ◽  
Lubia del Carmen Castillo-Arcos ◽  
Leticia Cortaza-Ramírez
Keyword(s):  
Web Of Science ◽  
Indigenous Population ◽  
Indigenous Populations ◽  
Factors Associated ◽  
The Family ◽  
Different Types ◽  
Human Care ◽  
Ebsco Host ◽  
Nursing Professionals ◽  
Consequences Of Violence

Abstract OBJECTIVE To analyze publications of qualitative studies that addressed the phenomenon of violence in indigenous population. METHOD Meta-synthesis of studies published in the period of 2006 to 2016, with search in the Ebsco Host, Cuiden Plus, Science Direct, Springer, and Web of Science databases. RESULTS A new reinterpretation of the findings was generated from the codes and categories of the primary articles. Five categories emerged: living violence, factors associated with patterns of violence, consequences of violence, interaction dynamics in situations of violence, and how to deal with violence. CONCLUSIONS Indigenous people experience different types of violence at an early age; experienced in the family. This makes it an emerging social problem that must be taken care of urgently and represents an area of opportunity for the nursing professionals whose central focus is human care.

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