scholarly journals Composition and Diversity of CRISPR-Cas13a systems in the genus Leptotrichia

2019 ◽  
Author(s):  
Shinya Watanabe ◽  
Bintao Cui ◽  
Kotaro Kiga ◽  
Yoshifumi Aiba ◽  
Xin-Ee Tan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Host Cell ◽  
Type I ◽  
Whole Genome ◽  
Type Ii ◽  
Genome Sequences ◽  
Type Iv ◽  
Rna Targeting ◽  
Sequence Similarities

AbstractClustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting CRISPR-Cas system and has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities, which was first identified in Leptotrichia shahii CRISPR-Cas13a. Here, the complete whole genome sequences of 11 Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a and other CRISPR-Cas systems. Various types of CRISPR-Cas systems, I-B, II-C, III-A, III-D, III-like and VI-A, were unevenly distributed among the Leptotrichia genomes, accounting for 10 (34.4%), 1 (2.6%), 6 (15.4%), 6 (15.4%), 3 (7.7%) and 11 (37.9%) of the 29 strains, respectively, while 8 (20.5%) strains had no CRISPR-Cas system. The Cas13a effectors were highly divergent with amino acid sequence similarities ranging from 61% to 90% to that of L. shahii and their collateral ssRNA cleavage activities, resulting in cytotoxicity to host cell, were found to be maintained. CRISPR-Cas spacers represent a sequential achievement of former intruder encounters, and the retained spacers reflect the evolutionary phylogeny or relatedness of strains. Analysis of spacer contents and numbers among Leptotrichia species showed considerable diversity with only 2 (0.5%) of 400 spacers through CRIPSR-Cas I-VI were shared by two strains. The organisation and distribution of CRISPR-Cas systems (type I-VI) encoded by all registered Leptotrichia species revealed that effector or spacer sequences of the CRISPR-Cas systems were very divergent, and the prevalence of types I, III and VI was almost equal. There was only one strain carrying type II, while none carried type IV or V. These results provide new insights into the characteristics and divergences of CRISPR-Cas systems among Leptotrichia species.

scholarly journals The amino acid sequence of component 7c, a type II intermediate-filament protein from wool

1989 ◽  
Vol 261 (3) ◽  
pp. 1015-1022 ◽  
Author(s):  
L G Sparrow ◽  
C P Robinson ◽  
D T W McMahon ◽  
M R Rubira
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Intermediate Filament ◽  
Coiled Coil ◽  
British Library ◽  
Intermediate Filament Protein ◽  
Type I ◽  
Type Ii ◽  
Blocking Group ◽  
Intermediate Filament Proteins

Component 7c is one of the four homologous type II intermediate-filament proteins that, by association with the complementary type I proteins, form the microfibrils or intermediate filaments in wool. Component 7c was isolated as the S-carboxymethyl derivative from Merino wool and its amino acid sequence was determined by manual and automatic sequencing of peptides produced by chemical and enzymic cleavage reactions. It is an N-terminally blocked molecule of 491 residues and Mr (not including the blocking group) of 55,600; the nature of the blocking group has not been determined. The predicted secondary structure shows that component 7c conforms to the now accepted pattern for intermediate-filament proteins in having a central rod-like region of approximately 310 residues of coiled-coil alpha-helix flanked by non-helical N-and C-terminal regions. The central region is divided by three non-coiled-coil linking segments into four helical segments 1A, 1B, 2A and 2B. The N-and C-terminal non-helical segments are 109 and 71 residues respectively and are rich in cysteine. Details of procedures use in determining the sequence of component 7c have been deposited as a Supplementary Publication SUP 50152 (65 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257,5. The information comprises: (1) details of chemical and enzymic methods used for cleavage of component 7c, peptides CN1, CN2 and CN3, and various other peptides, (2) details of the procedures used for the fractionation and purification of peptides from (1), including Figures showing the elution profiles from the chromatographic steps used, (3) details of methods used to determine the C-terminal sequence of peptide CN3, and (4) detailed evidence to justify a number of corrections to the previously published sequence.

scholarly journals The complete cDNA and deduced amino acid sequence of a type II mouse epidermal keratin of 60,000 Da: analysis of sequence differences between type I and type II keratins.

1984 ◽  
Vol 81 (18) ◽  
pp. 5709-5713 ◽  
Author(s):  
P. M. Steinert ◽  
D. A. Parry ◽  
E. L. Racoosin ◽  
W. W. Idler ◽  
A. C. Steven ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Type I ◽  
Type Ii

scholarly journals Protein pI and Intracellular Localization

2021 ◽  
Vol 8 ◽  
Author(s):  
Alexander A. Tokmakov ◽  
Atsushi Kurotani ◽  
Ken-Ichi Sato
Keyword(s):  
Experimental Data ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Subcellular Localization ◽  
Computational Analysis ◽  
Intracellular Localization ◽  
Data Availability ◽  
Whole Genome ◽  
Genome Sequences ◽  
Good Agreement

The protein isoelectric point (pI) can be calculated from an amino acid sequence using computational analysis in a good agreement with experimental data. Availability of whole-genome sequences empowers comparative studies of proteome-wide pI distributions. It was found that the whole-proteome distributions of protein pI values are multimodal in different species. It was further hypothesized that the observed multimodality is associated with subcellular localization-specific differences in local pI distributions. Here, we overview the multimodality of proteome-wide pI distributions in different organisms focusing on the relationships between protein pI and subcellular localization. We also discuss the probable factors responsible for variation of the intracellular localization-specific pI profiles.

scholarly journals Draft Genome Sequences ofMycobacterium kansasiiStrains 1010001454, 1010001458, 1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental Sources

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Dominik Strapagiel ◽  
Paulina Borówka ◽  
Błażej Marciniak ◽  
Zofia Bakuła ◽  
Jakko van Ingen ◽  
...  
Keyword(s):  
Opportunistic Infections ◽  
Nontuberculous Mycobacteria ◽  
Draft Genome ◽  
European Countries ◽  
Type I ◽  
Type Ii ◽  
Mycobacterium Kansasii ◽  
Genome Sequences ◽  
Type Iv ◽  
Type V

Mycobacterium kansasiibelongs to the nontuberculous mycobacteria (NTM) and causes opportunistic infections with both pulmonary and extrapulmonary manifestations. Here, we report the draft genome sequences of six environmentalM. kansasiistrains, designated 1010001495 (type I), 1010001469 (type II), 1010001468 (type III), 1010001458 (type IV), 1010001454 (type V), and 1010001493 (type V), originally isolated in five different European countries.

Labelling of non-A, non-B hepatitis infected chimpanzee hepatocytes with nuclease-gold conjugates

1984 ◽  
Vol 42 ◽  
pp. 250-251
Author(s):  
G. D. Gagne ◽  
M. F. Miller ◽  
D. A. Peterson
Keyword(s):  
Endoplasmic Reticulum ◽  
Experimental Infection ◽  
Uranyl Acetate ◽  
Type I ◽  
Cellular Injury ◽  
Type Ii ◽  
Tubular Structures ◽  
Type Iii ◽  
Type Iv ◽  
Infected Chimpanzee

Experimental infection of chimpanzees with non-A, non-B hepatitis (NANB) or with delta agent hepatitis results in the appearance of characteristic cytoplasmic alterations in the hepatocytes. These alterations include spongelike inclusions (Type I), attached convoluted membranes (Type II), tubular structures (Type III), and microtubular aggregates (Type IV) (Fig. 1). Type I, II and III structures are, by association, believed to be derived from endoplasmic reticulum and may be morphogenetically related. Type IV structures are generally observed free in the cytoplasm but sometimes in the vicinity of type III structures. It is not known whether these structures are somehow involved in the replication and/or assembly of the putative NANB virus or whether they are simply nonspecific responses to cellular injury. When treated with uranyl acetate, type I, II and III structures stain intensely as if they might contain nucleic acids. If these structures do correspond to intermediates in the replication of a virus, one might expect them to contain DNA or RNA and the present study was undertaken to explore this possibility.

scholarly journals Brachial supporting structure of Spiriferida (Brachiopoda)

2020 ◽  
pp. 1-15
Author(s):  
Zhiwei Yuan ◽  
Wen Guo ◽  
Dan Lyu ◽  
Yuanlin Sun
Keyword(s):  
Mantle Cavity ◽  
Family Type ◽  
Type I ◽  
Type Ii ◽  
Feeding Apparatus ◽  
Single Family ◽  
Supporting Structure ◽  
Type Iii ◽  
Type Iv ◽  
Evolutionary Lineages

Abstract The filter-feeding organ of some extinct brachiopods is supported by a skeletal apparatus called the brachidium. Although relatively well studied in Atrypida and Athyridida, the brachidial morphology is usually neglected in Spiriferida. To investigate the variations of brachidial morphology in Spiriferida, 65 species belonging to eight superfamilies were analyzed. Based on the presence/absence of the jugal processes and normal/modified primary lamellae of the spiralia, four types of brachidium are recognized. Type-I (with jugal processes) and Type-II (without jugal processes), both having normal primary lamellae, could give rise to each other by losing/re-evolving the jugal processes. Type-III, without jugal processes, originated from Type-II through evolution of the modified lateral-convex primary lamellae, and it subsequently gave rise to Type-IV by evolving the modified medial-convex primary lamellae. The evolution of brachidia within individual evolutionary lineages must be clarified because two or more types can be present within a single family. Type-III and Type-IV are closely associated with the prolongation of the crura, representing innovative modifications of the feeding apparatus in response to possible shift in the position of the mouth towards the anterior, allowing for more efficient feeding on particles entering the mantle cavity from the anterior gape. Meanwhile, the modified primary lamellae adjusted/regulated the feeding currents. The absence of spires in some taxa with Type-IV brachidium might suggest that they developed a similar lophophore to that in some extant brachiopods, which can extend out of the shell.

scholarly journals Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Sara Jones ◽  
Raji Prasad ◽  
Anjana S. Nair ◽  
Sanjai Dharmaseelan ◽  
Remya Usha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Analysis ◽  
Influenza A ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
H1n1 Pandemic ◽  
Genome Sequences ◽  
Influenza A H1n1 ◽  
Virus Isolates ◽  
New Mutations

ABSTRACT We report here the whole-genome sequence of six clinical isolates of influenza A(H1N1)pdm09, isolated from Kerala, India. Amino acid analysis of all gene segments from the A(H1N1)pdm09 isolates obtained in 2014 and 2015 identified several new mutations compared to the 2009 A(H1N1) pandemic strain.

Response properties of units in the dorsal cochlear nucleus of unanesthetized decerebrate gerbil

1996 ◽  
Vol 75 (4) ◽  
pp. 1411-1431 ◽  
Author(s):  
K. A. Davis ◽  
J. Ding ◽  
T. E. Benson ◽  
H. F. Voigt
Keyword(s):  
Dorsal Cochlear Nucleus ◽  
Type I ◽  
Type Ii ◽  
Decerebrate Cat ◽  
Excitatory Response ◽  
Type Iii ◽  
Type Iv ◽  
Noise Type ◽  
Rate Versus ◽  
Excitatory Responses

1. The electrophysiological responses of single units in the dorsal cochlear nucleus of unanesthetized decerebrate Mongolian gerbil (Meriones unguiculatus) were recorded. Units were classified according to the response map scheme of Evans and Nelson as modified by Young and Brownell, Young and Voigt, and Shofner and Young. Type II units have a V-shaped excitatory response map similar to typical auditory nerve tuning curves but little or no spontaneous activity (SpAc < 2.5 spikes/s) and little or no response to noise. Type I/III units also have a V-shaped excitatory map and SpAc < 2.5 spikes/s, but have an excitatory response to noise. Type III units have a V-shaped excitatory map with inhibitory sidebands, SpAc > 2.5 spikes/s, and an excitatory response to noise. Type IV-T units typically also have a V-shaped excitatory map with inhibitory sidebands, but have a highly nonmonotonic rate versus level response to best frequency (BF) tones like type IV units, SpAc > 2.5 spikes/s, and an excitatory response to noise. Type IV units have a predominantly inhibitory response map above an island of excitation of BF, SpAc > 2.5 spikes/s, and an excitatory response to noise. We present results for 133 units recorded with glass micropipette electrodes. The purpose of this study was to establish a normative response map data base in this species for ongoing structure/function and correlation studies. 2. The major types of units (type II, type I/III, type III, type IV-T, and type IV) found in decerebrate cat are found in decerebrate gerbil. However, the percentage of type II (7.5%) and type IV (11.3%) units encountered are smaller and the percentage of type III (62.4%) units is larger in decerebrate gerbil than in decerebrate cat. In comparison, Shofner and Young found 18.5% type II units, 30.6% type IV units, and 23.1% type III units using metal electrodes. 3. Two new unit subtypes are described in gerbil: type III-i and type IV-i units. Type III-i units are similar to type III units except that type III-i units are inhibited by low levels of noise and excited by high levels of noise whereas type III units have strictly excitatory responses to noise. Type IV-i units are similar to type IV units except that type IV-i units are excited by low levels of noise and become inhibited by high levels of noise whereas type IV units have strictly excitatory responses to noise. Type III-i units are approximately 30% of the type III population and type IV-i units are approximately 50% of the type IV population. 4. On the basis of the paucity of classic type II units and the reciprocal responses to broadband noise of type III-i and type IV-i units, we postulate that some gerbil type III-i units are the same cell type and have similar synaptic connections as cat type II units. 5. Type II and type I/III units are distinguished from one another on the basis of both their relative noise response, rho, and the normalized slope of the BF tone rate versus level functions beyond the first maximum. Previously, type II units were defined to be those nonspontaneously active units with rho values < 0.3 where rho is defined as the ratio of the maximum noise response minus spontaneous rate to the maximum BF tone response minus spontaneous rate. In the gerbil, the average rho value for type II units is 0.25, although a few values are > 0.3, and the rate-level curves are consistently nonmonotonic with normalized slopes steeper than than -0.007/dB. The average rho value for type I/III units is 0.54, although a few values are < 0.3, and the rate-level curves tend to saturate with slopes shallower than -0.006/dB. In general, the response properties of type II units recorded in gerbil are similar to those recorded in decerebrate cat. 6. In comparison to decerebrate cat, the lower percentage of type IV units recorded in decerebrate gerbil may be due to a species difference (a reduced number of type II units in gerbil) or an electrode bias.

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