Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution

The analysis of bacterial genomes is a potent tool to investigate the distribution of specific traits related to the ability of surviving in particular environments. Among the traits associated with the adaptation to hostile conditions, toxin–antitoxin (TA) systems have recently gained attention in lactic acid bacteria. In this work, genome sequences of Lacticaseibacillus strains of dairy origin were compared, focusing on the distribution of type I TA systems homologous to Lpt/RNAII and of the most common type II TA systems. A high number of TA systems have been identified spread in all the analyzed strains, with type I TA systems mainly located on plasmid DNA. The type II TA systems identified in these strains highlight the diversity of encoded toxins and antitoxins and their organization. This study opens future perspectives on the use of genomic data as a resource for the study of TA systems distribution and prevalence in microorganisms of industrial relevance.

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Patterns of Aneurysm Recurrence After Microsurgical Clip Obliteration

Neurosurgery ◽

10.1227/neu.0b013e318276b46b ◽

2012 ◽

Vol 72 (1) ◽

pp. 65-69 ◽

Cited By ~ 14

Author(s):

Alejandro M. Spiotta ◽

Ferdinand Hui ◽

Albert Schuette ◽

Shaye I. Moskowitz

Keyword(s):

Retrospective Review ◽

Intracranial Aneurysms ◽

Common Type ◽

Type I ◽

Type Ii ◽

Viable Option ◽

Type Iii ◽

Clip Application

Abstract BACKGROUND: Microsurgical clip obliteration remains a time-honored and viable option for the treatment of select aneurysms with very low rates of recurrence. OBJECTIVE: We studied previously clipped aneurysms that were found to have recurrences to better understand the patterns and configurations of these rare entities. METHODS: A retrospective review was performed of 2 prospectively maintained databases of aneurysm treatments from 2 institutions spanning 14 years to identify patients with recurrence of previously clipped intracranial aneurysms. RESULTS: Twenty-six aneurysm recurrences were identified. Three types of recurrence were identified: type I, proximal to the clip tines; type II, distal; and type III, lateral. The most common type of recurrence was that arising distal to the clip tines (46.1%), and the least frequently encountered recurrence was that arising proximal to the tines (19.2%). Laterally located recurrences were found in 34.6% of cases. CONCLUSION: We describe 3 different patterns of aneurysm recurrence with respect to clip application: those occurring proximal, distal, or lateral to the clip tines.

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Maintenance of chondrocyte phenotype during expansion on PLLA microtopographies

Journal of Tissue Engineering ◽

10.1177/2041731418789829 ◽

2018 ◽

Vol 9 ◽

pp. 204173141878982 ◽

Cited By ~ 6

Author(s):

Elisa Costa ◽

Cristina González-García ◽

José Luis Gómez Ribelles ◽

Manuel Salmerón-Sánchez

Keyword(s):

Lactic Acid ◽

Type I Collagen ◽

Collagen Type ◽

Articular Chondrocytes ◽

Collagen Type I ◽

Cell Phenotype ◽

Type I ◽

Type Ii ◽

Collagen Type Ii ◽

Chondrocyte Phenotype

Articular chondrocytes are difficult to grow, as they lose their characteristic phenotype following expansion on standard tissue culture plates. Here, we show that culturing them on surfaces of poly(L-lactic acid) of well-defined microtopography allows expansion and maintenance of characteristic chondrogenic markers. We investigated the dynamics of human chondrocyte dedifferentiation on the different poly(L-lactic acid) microtopographies by the expression of collagen type I, collagen type II and aggrecan at different culture times. When seeded on poly(L-lactic acid), chondrocytes maintained their characteristic hyaline phenotype up to 7 days, which allowed to expand the initial cell population approximately six times without cell dedifferentiation. Maintenance of cell phenotype was afterwards correlated to cell adhesion on the different substrates. Chondrocytes adhesion occurs via the α5 β1 integrin on poly(L-lactic acid), suggesting cell–fibronectin interactions. However, α2 β1 integrin is mainly expressed on the control substrate after 1 day of culture, and the characteristic chondrocytic markers are lost (collagen type II expression is overcome by the synthesis of collagen type I). Expanding chondrocytes on poly(L-lactic acid) might be an effective solution to prevent dedifferentiation and improving the number of cells needed for autologous chondrocyte transplantation.

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Study of Acromial Shapes in Relation to Gender

National Journal of Clinical Anatomy ◽

10.1055/s-0039-1693288 ◽

2019 ◽

Vol 08 (02) ◽

pp. 087-090

Author(s):

Pushpa Nagavalli Basavanna ◽

Roshni Bajpe

Keyword(s):

Common Type ◽

Subacromial Impingement Syndrome ◽

Type I ◽

Type Ii ◽

Medical Sciences ◽

Female Adult ◽

Male And Female ◽

Type Iv ◽

Flat Type ◽

Shoulder Pathologies

Abstract Introduction Subacromial impingement syndrome is considered to be one of the most common musculoskeletal disorders affecting the shoulder joint. The objectives of the study were to find out the morphology of acromion process and the presence of enthesophytes in male and female scapulae. Methodology The study was done on 100 male and 100 female adult dry human scapulae of different people, collected from the Department of Anatomy, Kempegowda Institute of Medical Sciences, Bangalore. Acromial shapes were classified into 4 types—type I (flat), type II (curved), type III (hooked), and type IV (convex). Acromial spurs (enthesophytes), if any, in the anterior one-third of acromion was noted. Results The most common type of acromion found in both the sexes is type I. Even the enthesophytes were more commonly associated with type I acromion. The study revealed that the acromial shape of dried scapulae did not vary significantly with sex. Conclusion In the present study we could find the four types of acromion mentioned in the literature. Since acromial shapes influence the shoulder pathologies involving acromion, the knowledge on acromial morphology and enthesophytes aid the clinicians during its diagnoses and treatment (acromioplasty). Also, data on morphology of acromion could be used for forensic and anthropological purposes for determining gender, ethnicity, and so forth.

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Morphological characteristics of the plantar calcaneocuboid ligaments

Journal of Foot and Ankle Research ◽

10.1186/s13047-020-00443-7 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Mutsuaki Edama ◽

Tomoya Takabayashi ◽

Hirotake Yokota ◽

Ryo Hrabayashi ◽

Chie Sekine ◽

...

Keyword(s):

Fiber Bundle ◽

Morphological Characteristics ◽

Common Type ◽

Morphological Features ◽

Fiber Bundles ◽

Type I ◽

Functional Difference ◽

Type Ii ◽

Functional Differences ◽

The Difference

Abstract Background The aim of this study was to clarify the differences in morphological features between the long plantar ligament (LPL) and the short plantar ligament (SPL). Methods This investigation examined 50 legs from 25 Japanese cadavers. The LPL and SPL of each leg were classified into one of three types based on the shape and number of fiber bundles. Then, fiber bundle length, fiber bundle width, and fiber bundle thickness were measured. Results The LPL was rectangular in shape (Type I) in 12%, hourglass shape (Type II) in 62%, and triangular in shape (Type III) in 26%. The SPL was a single fiber bundle (Type I-a) in 26%, a surface fiber bundle and a deep fiber bundle (Type I-b) in 60%, and a surface fiber bundle (medial and lateral) and a deep fiber bundle (Type II) in 14%. Regarding the morphological characteristics, there were no significant differences among the types in the LPL, but there were differences between types and between surface and deep fiber bundles in the SPL. Conclusions For the LPL, the hourglass shape is the most common type. However, there appeared to be no functional difference due to the difference in the shape of the LPL, since there were no significant differences among the types in the LPL. For the SPL, there were types of single, double and triple fiber bundles; there may be functional differences based on the number of fiber bundles and between superficial and deep fibers.

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RGD-Dendrimer-Poly(L-lactic) Acid Nanopatterned Substrates for the Early Chondrogenesis of Human Mesenchymal Stromal Cells Derived from Osteoarthritic and Healthy Donors

Materials ◽

10.3390/ma13102247 ◽

2020 ◽

Vol 13 (10) ◽

pp. 2247

Author(s):

Cristina Rodríguez-Pereira ◽

Anna Lagunas ◽

Ignasi Casanellas ◽

Yolanda Vida ◽

Ezequiel Pérez-Inestrosa ◽

...

Keyword(s):

Lactic Acid ◽

Mesenchymal Stromal Cells ◽

Stromal Cells ◽

Connexin 43 ◽

Collagen Type ◽

Type I ◽

Type Ii ◽

Collagen Type Ii ◽

Junction Protein ◽

Cell Pellet

Aiming to address a stable chondrogenesis derived from mesenchymal stromal cells (MSCs) to be applied in cartilage repair strategies at the onset of osteoarthritis (OA), we analyzed the effect of arginine–glycine–aspartate (RGD) density on cell condensation that occurs during the initial phase of chondrogenesis. For this, we seeded MSC-derived from OA and healthy (H) donors in RGD-dendrimer-poly(L-lactic) acid (PLLA) nanopatterned substrates (RGD concentrations of 4 × 10−9, 10−8, 2.5 × 10−8, and 10−2 w/w), during three days and compared to a cell pellet conventional three-dimensional culture system. Molecular gene expression (collagens type-I and II–COL1A1 and COL2A1, tenascin-TNC, sex determining region Y-box9-SOX9, and gap junction protein alpha 1–GJA1) was determined as well as the cell aggregates and pellet size, collagen type-II and connexin 43 proteins synthesis. This study showed that RGD-tailored first generation dendrimer (RGD-Cys-D1) PLLA nanopatterned substrates supported the formation of pre-chondrogenic condensates from OA- and H-derived human bone marrow-MSCs with enhanced chondrogenesis regarding the cell pellet conventional system (presence of collagen type-II and connexin 43, both at the gene and protein level). A RGD-density dependent trend was observed for aggregates size, in concordance with previous studies. Moreover, the nanopatterns’ had a higher effect on OA-derived MSC morphology, leading to the formation of bigger and more compact aggregates with improved expression of early chondrogenic markers.

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Hearing loss and pigmentary disturbances in Waardenburg syndrome with reference to WS Type II

The Journal of Laryngology & Otology ◽

10.1017/s002221510012938x ◽

1995 ◽

Vol 109 (2) ◽

pp. 96-100 ◽

Cited By ~ 9

Author(s):

Xuezhong Liu ◽

Valerie Newton ◽

Andrew Read

Keyword(s):

Hearing Loss ◽

Common Type ◽

Hearing Impaired ◽

Type I ◽

Type Ii ◽

Waardenburg Syndrome ◽

Profound Hearing Loss ◽

Significant Difference ◽

Impaired Group ◽

Pigmentation Disorders

AbstractThirty families in which there were 149 individuals affected by the Waardenburg syndrome (WS) were investigated for penetrance of hearing loss and pigmentary abnormalities. Twenty two families contained 89 individuals affected by WS Type II and eight families with 60 individuals affected by Type I. A bilateral symmetrical sensorineural hearing loss was found to be the most common type of hearing loss. The most frequent degree of hearing loss category was a hearing loss of > 100dB HL with no difference between syndrome types.Although there was no significant difference in the frequency of pigmentation disorders between Type I and II, considering these abnormalities as a whole, heterochromia irides was more common in Type II than Type I and other pigmentation disorders were more frequent in Type I: 62 per cent of Type I patients had more than one pigmentary defect, but only 28 per cent of Type II. Pigmentary disturbances were not significantly more frequent in the hearing impaired group than in the normally hearing group in either Type I or II when taking into account the occurrence of only one pigmentation disorder. There was a significantly higher proportion of pigmentary defects in the hearing impaired group with Type I when only those having more than one pigmentary abnormality were compared: 93.3 per cent of Type I patients and 88.5 per cent of Type II patients with a profound hearing loss had pigmentary defects. The frequency of pigmentation disorders was not greater when the hearing loss was more severe in either type. Penetrance for hearing loss and pigmentary abnormalities showed marked intrafamilial and interfamilial variation.

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Harnessing the CRISPR-Cas Systems to Combat Antimicrobial Resistance

Frontiers in Microbiology ◽

10.3389/fmicb.2021.716064 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cheng Duan ◽

Huiluo Cao ◽

Lian-Hui Zhang ◽

Zeling Xu

Keyword(s):

Immune System ◽

Antimicrobial Resistance ◽

Global Health ◽

Adaptive Immune System ◽

Type I ◽

Type Ii ◽

Bacterial Genomes ◽

Adaptive Immune ◽

The Past ◽

Attractive Option

The emergence of antimicrobial-resistant (AMR) bacteria has become one of the most serious threats to global health, necessitating the development of novel antimicrobial strategies. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system, known as a bacterial adaptive immune system, can be repurposed to selectively target and destruct bacterial genomes other than invasive genetic elements. Thus, the CRISPR-Cas system offers an attractive option for the development of the next-generation antimicrobials to combat infectious diseases especially those caused by AMR pathogens. However, the application of CRISPR-Cas antimicrobials remains at a very preliminary stage and numerous obstacles await to be solved. In this mini-review, we summarize the development of using type I, type II, and type VI CRISPR-Cas antimicrobials to eradicate AMR pathogens and plasmids in the past a few years. We also discuss the most common challenges in applying CRISPR-Cas antimicrobials and potential solutions to overcome them.

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Diversification of the restriction–modification system of Streptococcus pyogenes through its acquisition of mobile elements

10.1101/2020.06.30.179317 ◽

2020 ◽

Author(s):

Atsushi Ota ◽

Yukiko Nishiuchi ◽

Noriko Nakanishi ◽

Yoshio Iijima ◽

Tomotada Iwamoto ◽

...

Keyword(s):

Streptococcus Pyogenes ◽

Complete Genome ◽

Type I ◽

Sequence Specificity ◽

Type Ii ◽

Genome Sequences ◽

Modification System ◽

Dna Sequence Specificity ◽

Restriction Modification System ◽

Restriction Modification

ABSTRACTRestriction–modification (RM) systems are typically regarded as “primitive immune systems” in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity in Streptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels in S. pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity in S. pyogenes.

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

10.1101/710533 ◽

2019 ◽

Cited By ~ 1

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.

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Morphological Characteristics of the Plantar Calcaneocuboid Ligaments

10.21203/rs.3.rs-102037/v1 ◽

2020 ◽

Author(s):

Mutsuaki Edama ◽

Tomoya Takabayashi ◽

Hirotake Yokota ◽

Ryo Hirabayashi ◽

Chie Sekine ◽

...

Keyword(s):

Fiber Bundle ◽

Morphological Characteristics ◽

Common Type ◽

Morphological Features ◽

Fiber Bundles ◽

Type I ◽

Functional Difference ◽

Type Ii ◽

Functional Differences ◽

The Difference

Abstract Background: The aim of this study was to clarify the differences in morphological features based on differences in the shape and number of the long plantar ligament (LPL) and the short plantar ligament (SPL).Methods: This investigation examined 50 legs from 25 Japanese cadavers. The LPL and SPL of each leg were classified into one of three types based on the shape and number of fiber bundles. Then, fiber bundle length, fiber bundle width, and fiber bundle thickness were measured.Results: The LPL was rectangular in shape (Type I) in 12%, hourglass shape (Type II) in 62%, and triangular in shape (Type III) in 26%. The SPL was a single fiber bundle (Type I-a) in 26%, a surface fiber bundle and a deep fiber bundle (Type I-b) in 60%, and a surface fiber bundle (medial and lateral) and a deep fiber bundle (Type II) in 14%. Regarding the morphological characteristics, there were no significant differences among the types in the LPL, but there were differences between types and between surface and deep fiber bundles in the SPL.Conclusions: For the LPL, the hourglass shape is the most common type. However, there appeared to be no functional difference due to the difference in the shape of the LPL, since there were no significant differences among the types in the LPL. For the SPL, there were types of single, double and triple fiber bundles; there may be functional differences based on the number of fiber bundles and between superficial and deep fibers.

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