Corrigendum: Genetic characteristics and integration specificity of Salmonella enterica temperate phages

[This corrects the article DOI: 10.3389/fmicb.2023.1199843.].

Anatomical Study of Sites and Surface Area of the Attachment Region of Tibial Posterior Tendon Attachment

BACKGROUND

The purpose of this study was not only to examine the attachment site but also to quantify the effect of the tibialis posterior tendon (TPT) on each attachment site by examining the surface area of the attachment region.

METHODS

We examined 100 feet from 50 Japanese cadavers. The TPT attachment to the navicular bone (NB), medial cuneiform bone (MCB), and lateral cuneiform bone (LCB) were set as the main attachment sites (Type I). The attachment seen in Type I with the addition of one additional site of attachment was defined as Type II. Furthermore, surface area was measured using a three-dimensional scanner.

RESULTS

Attachment to the NB, MCB, and LCB was present in all specimens. The TPT attachment to the NB, MCB, and LCB comprised 75.1% of total attachment surface area. The ratio of the NB, MCB, and LCB in each type was about 90% in Types II and III, and 70-80% in Types IV-VII.

CONCLUSION

The quantitative results demonstrated the NB, MCB, and LCB to be the main sites of TPT attachment, although individual differences in attachment sites exist, further developing the findings of previous studies.

Site-specific glycosylation of proteoglycans: a revisited frontier in proteoglycan research

Proteoglycans (PGs), a class of carbohydrate-modified proteins, are present in essentially all metazoan organisms investigated to date. PGs are composed of glycosaminoglycan (GAG) chains attached to various core proteins and are important for embryogenesis and normal homeostasis. PGs exert many of their functions via their GAG chains and understanding the details of GAG-ligand interactions has been an essential part of PG research. Although PGs are also involved in many diseases, the number of GAG-related drugs used in the clinic is yet very limited, indicating a lack of detailed structure-function understanding. Structural analysis of PGs has traditionally been obtained by first separating the GAG chains from the core proteins, after which the two components are analyzed separately. While this strategy greatly facilitates the analysis, it precludes site-specific information and introduces either a "GAG" or a "core protein" perspective on the data interpretation. Mass-spectrometric (MS) glycoproteomic approaches have recently been introduced, providing site-specific information on PGs. Such methods have revealed a previously unknown structural complexity of the GAG linkage regions and resulted in identification of several novel CSPGs and HSPGs in humans and in model organisms, thereby expanding our view on PG complexity. In light of these findings, we discuss here if the use of such MS-based techniques, in combination with various functional assays, can also be used to expand our functional understanding of PGs. We have also summarized the site-specific information of all human PGs known to date, providing a theoretical framework for future studies on site-specific functional analysis of PGs in human pathophysiology.

Host Range, Morphology and Sequence Analysis of Ten Temperate Phages Isolated from Pathogenic Yersinia enterocolitica Strains

Yersinia enterocolitica is a heterogeneous species comprising highly pathogenic, weakly pathogenic and non-pathogenic strains. Previous data suggest that gene exchange may occur in Yersinia. Only scarce information exists about temperate phages of Y. enterocolitica, even though many prophage sequences are present in this species. We have examined 102 pathogenic Y. enterocolitica strains for the presence of inducible prophages by mitomycin C treatment. Ten phages were isolated from nine strains belonging to the bio (B)/serotypes (O) B2/O:5,27, B2/O:9 and 1B/O:8. All phages are myoviruses showing lytic activity only at room temperature. Whole-genome sequencing of the phage genomes revealed that they belong to three groups, which, however, are not closely related to known phages. Group 1 is composed of five phages (type phage: vB_YenM_06.16.1) with genome sizes of 43.8 to 44.9 kb, whereas the four group 2 phages (type phage: vB_YenM_06.16.2) possess smaller genomes of 29.5 to 33.2 kb. Group 3 contains only one phage (vB_YenM_42.18) whose genome has a size of 36.5 kb, which is moderately similar to group 2. The host range of the phages differed significantly. While group 1 phages almost exclusively lysed strains of B2/O:5,27, phages of group 2 and 3 were additionally able to lyse B4/O:3, and some of them even B2/O:9 and 1B/O:8 strains.

A Systematic Review of Definitive Treatment for Inverted Papilloma Attachment Site and Associations With Recurrence

OBJECTIVE

Inverted papilloma (IP) is the most common benign neoplasm of the nasal cavity with known risk of recurrence. There is no standardized approach to definitive treatment for attachment sites. This systematic review aims to determine whether surgeon choice of technique differs by anatomic attachment site and whether different surgical techniques contribute to reduced rates of recurrence.

DATA SOURCES

PubMed and Ovid Medline.

REVIEW METHODS

A systematic review was conducted for studies reporting on IP. Those that included IP recurrence rates and primary tumor attachment site were reviewed.

RESULTS

Of 122 published studies, 14 met eligibility criteria, representing 585 patients and a recurrence rate of 5.8%. The maxillary sinus (50.9%) was the most common primary attachment site, and the sphenoid sinus was associated with the highest rate of recurrence (10.4%). The most utilized technique included debulking the tumor, removing mucosa over the attachment site, and drilling the underlying bone. The most common Krouse stage represented was T3 (53.3%). No single technique predicted a propensity for recurrence, but certain techniques are favored depending on IP attachment site. Finally, frozen sections to obtain evidence of clear margins intraoperatively significantly reduced rates of recurrence (3.4% vs 7.3%, P = .045).

CONCLUSION

Based on the current literature, the most common technique to address site of attachment involves resecting mucosa and drilling the tumor base. Choice of technique appears to differ for various sites of attachment. Use of intraoperative frozen section analysis appears to be associated with decreased recurrence overall.

LEVEL OF EVIDENCE

3.

Expanding the Chondroitin Sulfate Glycoproteome - But How Far?

Chondroitin sulfate proteoglycans (CSPGs) are found at cell surfaces and in connective tissues, where they interact with a multitude of proteins involved in various pathophysiological processes. From a methodological perspective, the identification of CSPGs is challenging, as the identification requires the combined sequencing of specific core proteins, together with the characterization of the CS polysaccharide modification(s). According to the current notion of CSPGs, they are often considered in relation to a functional role in which a given proteoglycan regulates a specific function in cellular physiology. Recent advances in glycoproteomic methods have, however, enabled the identification of numerous novel chondroitin sulfate core proteins, and their glycosaminoglycan attachment sites, in humans and in various animal models. In addition, these methods have revealed unexpected structural complexity even in the linkage regions. These findings indicate that the number and structural complexity of CSPGs are much greater than previously perceived. In light of these findings, the prospect of finding additional CSPGs, using improved methods for structural and functional characterizations, and studying novel sample matrices in humans and in animal models is discussed. Further, as many of the novel CSPGs are found in low abundance and with not yet assigned functions, these findings may challenge the traditional notion of defining proteoglycans. Therefore, the concept of proteoglycans is considered, discussing whether "a proteoglycan" should be defined mainly on the basis of an assigned function or on the structural evidence of its existence.

Inverted papilloma with multifocal attachment is associated with increased recurrence

BACKGROUND

Inverted papilloma (IP) is a benign sinonasal tumor with a well-known propensity to recur, especially at its bony attachment site. Anecdotal evidence suggests lower rate of recurrence in primary resection. We also aimed to evaluate the effect of multifocal vs single focus of attachment in disease control.

METHODS

This work is a retrospective review of 535 IP resections performed during the period from 2006 to 2016 at a tertiary-care center. Demographic data, tumor location and attachment sites, and follow-up duration data were obtained.

RESULTS

Two hundred ten patients were eligible for analysis. The mean age was 57 years, with an average postoperative surveillance of 36.4 months. Patients who had a previous procedure at an outside institution have a recurrence rate of 22.3%, compared with 12.4% for patients who had primary surgery at our institution. The most common site of attachment was maxillary sinus (47.6%), followed by ethmoid sinus (39%). Individual tumor review showed 50% of the patients to have multifocal attachment disease, of which there is a higher prevalence in secondary cases when compared with primary cases (53.7% vs 44.9%). Multiple tumor attachment sites had a significant effect on recurrence (odds ratio, 3.5; 95% confidence interval, 1.6-7.6; p = 0.002).

CONCLUSION

Primary resection and single-focus attachment of inverted papilloma are associated with lower recurrence rates at 3-year follow-up.

May the Phage be With You? Prophage-Like Elements in the Genomes of Soft Rot Pectobacteriaceae: Pectobacterium spp. and Dickeya spp

Soft Rot Pectobacteriaceae (SRP; Pectobacterium spp. and Dickeya spp., formerly known as pectinolytic Erwinia spp.) are necrotrophic bacterial pathogens infecting a large number of plant species worldwide, including agriculturally-important crops. Despite the SRP importance in agriculture, little is known about the bacteriophages infecting them, and even less about the prophages present in their genomes. Prophages are recognized as factors underlying bacterial virulence, genomic diversification and ecological fitness that contribute to the novel phenotypic properties of bacterial hosts. Likewise, they are recognized as a driving force of bacterial evolution. In this study, 57 complete genomes of Pectobacterium spp. and Dickeya spp. deposited in NCBI GenBank, were analyzed for the presence of prophage-like elements. Viral sequences were discovered in 95% of bacterial genomes analyzed with the use of PHASTER, PhiSpy, and manual curation of the candidate sequences using NCBI BLAST. In total 37 seemingly intact and 48 putatively defective prophages were found. The 37 seemingly intact prophages (27 sequences in Dickeya spp. genomes and 10 sequences in Pectobacterium spp. genomes) were annotated using RAST. Analysis of the prophage genes encoding viral structural proteins allowed classification of these prophages into different families of the order Caudovirales (tailed bacteriophages) with the SRP prophages of the Myoviridae family (81% of found prophages) being the most abundant. The phylogenetic relationships between prophages were analyzed using amino acid sequences of terminase large subunit (gene terL), integrase (gene int), holin (gene hol), and lysin (gene lys). None of these markers however proved fully useful for clear phylogenetic separation of prophages of SRP into distinct clades. Comparative analyses of prophage proteomes revealed six clusters: five present in Dickeya spp. and one within Pectobacterium spp. When screened for the presence of bacterial genes in the genomes of intact prophages, only one prophage did not contain any ORFs of bacterial origin, the other prophages contained up to 23 genes acquired from bacterial hosts. The bacterial genes present in prophages could possibly affect fitness and virulence of their hosts. The implication of prophage presence in the genomes of Pectobacterium spp. and Dickeya spp. is discussed.

Serine Integrase attP Binding and Specificity

Serine integrases catalyze the site-specific insertion of viral DNA into a host's genome. The minimal requirements and irreversible nature of this integration reaction have led to the use of serine integrases in applications ranging from bacterial memory storage devices to gene therapy. Our understanding of how the integrase proteins recognize the viral (attP) and host (attB) attachment sites is limited, with structural data available for only a Listeria integrase C-terminal domain (CTD) bound to an attP half-site. Here we report quantitative binding and saturation mutagenesis analyses for the Listeria innocua prophage attP site and a new 2.8-Å crystal structure of the CTD•attP half site. We find that Int binds with high affinity to attP (6.9 nM), but the Int CTD binds to attP half-sites with only 7- to 10-fold lower affinity, supporting the idea that free energy is expended to open an Int dimer for attP binding. Despite the 50-bp Int-attP interaction surface, only 20 residues are sensitive to mutagenesis, and of these, only 6 require a specific residue for efficient Int binding and integration activity. One of the integrase DNA-binding domains, the recombinase domain, appears to be primarily non-specific. Several substitutions result in an improved attP site, indicating that higher-efficiency attachment sites can be obtained through site engineering. These findings advance our understanding of serine integrase function and provide important data for efforts towards engineering this family of enzymes for a variety of biotechnology applications.

Excision and Circularization of Integrative Conjugative Element Tn5253 of Streptococcus pneumoniae

The integrative conjugative element (ICE) Tn5253 of Streptococcus pneumoniae, conferring resistance to tetracycline and chloramphenicol, was found integrated at a 83-bp specific target site (attB) located in the rbgA gene of the pneumococcal chromosome. PCR analysis of Tn5253-carrying strains showed evidence of precise excision of Tn5253 from the pneumococcal chromosome with production of (i) circular forms of the ICE in which the ends were joined by a 84-bp sequence (attTn), and (ii) reconstituted chromosomal attB. When integrated into the chromosome, Tn5253 was flanked by attL, identical to attB, and attR, identical to attTn. Circular forms of Tn5253 were present at a concentration of 3.8 × 10^-4 copies per chromosome, whereas reconstituted attB sites were at 3.0 × 10^-4 copies per chromosome. Deletion of int-xis of Tn5253 abolished production of circular forms (<7.1 × 10^-6 copies per chromosome) and was associated to the lack of Tn5253 conjugal transfer suggesting, as expected, that Tn5253 circular form acts as a conjugation intermediate.

Cortical Bony Thickening of the Lateral Intercondylar Wall: The Functional Attachment of the Anterior Cruciate Ligament

BACKGROUND

The anatomy of the anterior cruciate ligament (ACL) has become the subject of much debate. There has been extensive study into attachment points of the native ligament, especially regarding the femoral attachment. Some of these studies have suggested that fibers in the ACL are of differing functional importance. Fibers with higher functional importance would be expected to exert larger mechanical stress on the bone. According to Wolff's law, cortical thickening would be expected in these areas.

PURPOSE

To examine cortical thickening in the region of the ACL footprint (ie, the functional footprint of the ACL).

STUDY DESIGN

Descriptive laboratory study.

METHODS

Using micro-computed tomography with resolutions ranging from 71 to 91 μm, the cortical thickness of the lateral wall of the intercondylar notch in 17 cadaveric knees was examined, along with surface topography. After image processing, the relationship between the cortical thickening and surface topology was visually compared.

RESULTS

A pattern of cortical thickening consistent with the functional footprint of the ACL was found. On average, this area was 3 times thicker than the surrounding bone and significantly thicker than the remaining lateral wall ( P < .0001). This thickening was roughly elliptical in shape (with a mean centroid at 23.5 h:31 t on a Bernard and Hertel grid) and had areas higher on the wall where greater thickness was present. The relationship to previously reported osseous landmarks was variable, although the patterns were broadly consistent with those reported in previous studies describing direct and indirect fibers of the ACL.

CONCLUSION

The findings of this study are consistent with those of recent studies describing fibers in the ACL of differing functional importance. The area in which the thickening was found has been defined and is likely to represent the functional footprint of the ACL.

CLINICAL RELEVANCE

This information is of value to surgeons when determining the optimal place to position the femoral attachment site of the reconstructed ACL.

Linkers Having a Crucial Role in Antibody-Drug Conjugates

Antibody–drug conjugates (ADCs) comprised of a desirable monoclonal antibody, an active cytotoxic drug and an appropriate linker are considered to be an innovative therapeutic approach for targeted treatment of various types of tumors and cancers, enhancing the therapeutic parameter of the cytotoxic drug and reducing the possibility of systemic cytotoxicity. An appropriate linker between the antibody and the cytotoxic drug provides a specific bridge, and thus helps the antibody to selectively deliver the cytotoxic drug to tumor cells and accurately releases the cytotoxic drug at tumor sites. In addition to conjugation, the linkers maintain ADCs’ stability during the preparation and storage stages of the ADCs and during the systemic circulation period. The design of linkers for ADCs is a challenge in terms of extracellular stability and intracellular release, and intracellular circumstances, such as the acid environment, the reducing environment and cathepsin, are considered as the catalysts to activate the triggers for initiating the cleavage of ADCs. This review discusses the linkers used in the clinical and marketing stages for ADCs and details the fracture modes of the linkers for the further development of ADCs.

Ectoparasites of Propithecus diadema (Primates: Indriidae) With Notes on Unusual Attachment Site Selection by Haemaphysalis lemuris (Parasitiformes: Ixodidae)

An examination of ectoparasite loads in two populations of wild diademed sifakas, Propithecus diadema Bennett, yielded seven species-four mite species, a louse, a hippoboscid fly, and a leech. Prevalence of the tick Haemaphysalis lemuris Hoogstraal, the mites Liponyssella madagascariensis (Hirst) and Lemuralges propithecus Bochkov et al., and the louse Trichophilopterus babakotophilus Stobbe was quite high, at least 20%. H. lemuris was the most common ectoparasite in one population, while completely absent in a second one. When present, the most common attachment site for H. lemuris males was in the nares of their hosts.