Search

Summary: RNA transcribed at DNA double-strand breaks (DSBs) contributes to accurate DNA repair. Here, using the repair factors 53BP1 and TIRR as examples, we combine the fluorescence in situ hybridization (FISH) and proximity ligation assay (PLA) techniques to determine protein proximity to DSB-transcribed RNA. In this FISH-PLA protocol, we detail steps for designing DNA probes and image analysis using CellProfiler™ software. This approach has many potential applications for the study of the RNA-binding proteins and nascent RNA interactions.For complete details on the use and execution of this protocol, please refer to Ketley et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

ABSTRACT The Caatinga occupies an area of approximately 912,529 km², being one of the most distinct phytogeographic regions of the Brazilian territory. It has a vegetation that varies according to its distribution and relationship with the geography of each area. This study aimed to carry out a floristic survey of ABA farm, located in the municipality of Passagem, mesoregion of the Paraíba backlands. For four years, fortnightly botanical collections were carried out in all the plant's physiognomies on the farm, following a standard botanical protocol of floristic survey and herborization techniques. The results of this research brought up an important floristic list, consisting of 322 species from 194 genera belonging to 62 botanical families. Among these families, the ones with the higher number of species were Fabaceae (48 spp.), Euphorbiaceae (23 spp.), Convolvulaceae (21 spp.), Malvaceae (19 spp.) and Asteraceae (15 spp.). The habits were herbs (108 spp.), trees (59 spp.), subshrubs (56 spp.), shrubs (46 spp.), lianas (46 spp.), epyphytes and parasites (four spp.) In addition, 38 new species records were registered for the Paraíba State.

As doenças cardíacas estão entre as principais causas de óbito e o tratamento envolve mudanças de hábitos de vida e, em alguns casos, cirurgia. Durante o internamento, complicações podem ocorrer, a exemplo da diminuição da força muscular. A Mobilização Precoce (MP) intervém dando suporte para reverter ou minimizar essas complicações, porém, ainda assim, existem barreiras para sua realização. O objetivo do estudo foi avaliar o conhecimento de uma equipe de Unidade de Terapia Intensiva sobre a MP, evidenciando seus aspectos e possíveis barreiras para realização. Tratou-se de um estudo transversal de caráter observacional com abordagem exploratória, descritiva e delineamento quantitativo realizado com os profissionais da equipe da UTI Cardiológica de um Hospital Universitário na cidade de João Pessoa-PB. Foram entrevistados 27 profissionais das especialidades Fisioterapia, Medicina e Enfermagem, por meio da aplicação de um questionário estruturado, utilizando-se de respostas em uma escala tipo Likert, assim como de questões abertas. Os resultados evidenciaram que a maioria dos profissionais têm bom entendimento acerca da MP, dos efeitos da Imobilidade e da importância do trabalho em equipe. Em adição, a recusa do paciente e a falta de conhecimento sobre riscos e benefícios da realização foram elencadas como barreiras para realização da MP no serviço. Apesar dos resultados, foram identificadas divergências quanto a realização diária da MP, bem como do seguimento de protocolo do serviço, o que evidencia a necessidade de ações educativas continuadas.

The extensive genetic variation in the lipooligosaccharide (LOS) core biosynthesis gene cluster has led to the development of a classification system; with 8 classes (I-VIII) for Campylobacter coli (C. coli) LOS region and with 23 classes (A-W) or four groups (1-4) for Campylobacter jejuni (C. jejuni) LOS region. PCR based LOS locus type identification for C. jejuni clinical isolates from a UK hospital as well as in silico LOS locus analysis for C. jejuni and C. coli genome sequences from GenBank was carried out to determine the frequencies of various LOS genotypes in C. jejuni and C. coli. Analysis of LOS gene content in 60 clinical C. jejuni isolates and 703 C. jejuni genome sequences revealed that class B (Group 1) was the most abundant LOS class in C. jejuni. The hierarchy of C. jejuni LOS group prevalence (group 1 > group 2 > group 3 > group 4) as well as the hierarchy of the frequency of C. jejuni LOS classes present within the group 1 (B > C > A > R > M > V), group 2 (H/P > O > E > W), group 3 (F > K > S) and group 4 (G > L) was identified. In silico analysis of LOS gene content in 564 C. coli genome sequences showed class III as the most abundant LOS locus type in C. coli. In silico analysis of LOS gene content also identified three novel LOS types of C. jejuni and previously unknown LOS biosynthesis genes in C. coli LOS locus types I, II, III, V and VIII. This study provides C. jejuni and C. coli LOS loci class frequencies in a smaller collection of C. jejuni clinical isolates as well as within the larger, worldwide database of C. jejuni and C. coli.

Abstract Background Horses that undergo surgery for treatment of primary large colon disease have been reported to be at increased risk of developing recurrent colic episodes postoperatively. The reasons for this are currently unknown. The aim of the current study was to characterise the faecal microbiota of horses with colic signs associated with primary large colon lesions treated surgically and to compare the composition of their faecal microbiota to that of a control group of horses undergoing emergency orthopaedic treatment. Faecal samples were collected from horses in both groups on admission to hospital, during hospitalisation and following discharge from hospital for a total duration of 12 weeks. Additionally, colonic content samples were collected from surgical colic patients if pelvic flexure enterotomy was performed during laparotomy. A total of 12 samples were collected per horse. DNA was extracted from samples using a commercial kit. Amplicon mixtures were created by PCR amplification of the V1 – V2 regions of the bacterial 16S rRNA genes and submitted for sequencing using the Ion Torrent PGM next-generation sequencing system. Multivariate data analysis was used to characterise the faecal microbiota and to investigate differences between groups. Results Reduced species richness was evident in the colonic samples of the colic group compared to concurrent sampling of the faeces. Alpha and beta diversity differed significantly between the faecal and colonic microbiota with 304 significantly differentially abundant OTUs identified. Only 46 OTUs varied significantly between the colic and control group. There were no significant differences in alpha and beta diversity of faecal microbiota between colic and control horses at admission. However, this lack of significant differences between groups should be interpreted with caution due to a small sample size. Conclusions The results of the current study suggest that faecal samples collected at hospital admission in colic cases may not accurately represent changes in upper gut microbiota in horses with colic due to large colon disease.

Abstract We conducted a taxonomic survey of the Bignoniaceae from the “Fazenda Aba,” located at the municipality of Passagem, within the state of Paraiba (Northeastern Brazil). This inventory was based on material collected during monthly field expeditions between 2014 and 2017. For all collected species, we provide descriptions, information on the distribution, taxonomic comments, an identification key, illustrations, and photos. We recorded nine species distributed in six genera. The most representative genus is Tanaecium with three species, followed by Anemopaegma, with two species. The other four genera, Dolichandra, Fridericia, Handroanthus, and Tabebuia are represented by a single species each.

ABSTRACT Streptococcus pneumoniae is an asymptomatic colonizer of the nasopharynx, but it is also one of the most important bacterial pathogens of humans, causing a wide range of mild to life-threatening diseases. The basis of the pneumococcal transition from a commensal to a parasitic lifestyle is not fully understood. We hypothesize that exposure to host catecholamine stress hormones is important for this transition. In this study, we demonstrated that pneumococci preexposed to a hormone released during stress, norepinephrine (NE), have an increased capacity to translocate from the nasopharynx into the lungs compared to untreated pneumococci. Examination of NE-treated pneumococci revealed major alterations in metabolic profiles, cell associations, capsule synthesis, and cell size. By systemically mutating all 12 two-component and 1 orphan regulatory systems, we also identified a unique genetic regulatory circuit involved in pneumococcal recognition and responsiveness to human stress hormones. IMPORTANCE Microbes acquire unique lifestyles under different environmental conditions. Although this is a widespread occurrence, our knowledge of the importance of various host signals and their impact on microbial behavior is not clear despite the therapeutic value of this knowledge. We discovered that catecholamine stress hormones are the host signals that trigger the passage of Streptococcus pneumoniae from a commensal to a parasitic state. We identify that stress hormone treatment of this microbe leads to reductions in cell size and capsule synthesis and renders it more able to migrate from the nasopharynx into the lungs in a mouse model of infection. The microbe requires the TCS09 protein for the recognition and processing of stress hormone signals. Our work has particular clinical significance as catecholamines are abundant in upper respiratory fluids as well as being administered therapeutically to reduce inflammation in ventilated patients, which may explain why intubation in the critically ill is a recognized risk factor for the development of pneumococcal pneumonia.

Edible mushrooms have a number of medicinal properties and this study aimed to investigate the antimicrobial activity of Pleurotus eryngii DPUA1816 in metabolic broths after being grown in submerged cultivation. Mycelial fragments of pure P. eryngii culture was inoculated in sweet potato culture medium and incubated at 150 rpm for 15 days at 25°C. Pleurotus eryngii was also cultivated for 18 days under the same conditions, the mycelial biomass was separated by filtration for quantification. The supernatant was used in the diffusion test in agar and performed against Escherichia coli CCCD-E005, Staphylococcus aureus CCCD-S009, Pseudomonas aeruginosa CCCD-P004, Candida albicans CCCD-CC001, Candida parapsilosis CCCD-CC004 and Candida tropicalis CCCD-CC002. The samples showed no inhibitory activity against bacteria, however they showed some activity against C. albicans (12.17 mm), C. parapsilosis (27.67 mm) and C. tropicalis (13.67 mm). After being cultivated for 18 days, P. eryngii was able to inhibit all yeasts after 12 days of culture, with an inhibition halo of 29.33 mm at 16 days against C. parapsilosis. This study demonstrates the antifungal potential filtered liquids from P. eryngii cultivated in purple-skinned sweet potato culture medium, which suggests the possibility of the use of this species by the pharmaceutical industry as a natural source of biological action.

Mutation, diversity, natural selection and the biology of human pathogens (including antibiotic resistance) are key features of the biosciences curriculum at A Level and undergraduate study. Few resources exist to allow students to engage with these topics in an interactive manner. This paper describes an interactive, online simulation of mutation and of phase variation, a mechanism employed by many bacteria to generate genetic diversity, and includes an example of how the simulation can allow students to draw links between the genetics of pathogens and disease. Students experiment with different parameters of the simulation and use this--along with peer debate--to answer a set of questions. Use of the simulation goes some way to expel the fallacy that mutations are generated in response to environmental change. This freely available resource can be easily adapted to a wide range of audiences and topics where mutation is the underlying principle (cancer genetics for example).

Phase variation (PV) is a phenomenon common to a variety of bacterial species for niche adaption and survival in challenging environments. Among Campylobacter species, PV depends on the presence of intergenic and intragenic hypermutable G/C homopolymeric tracts. The presence of phase-variable genes is of especial interest for species that cause foodborne or zoonotic infections in humans. PV influences the formation and the structure of the lipooligosaccharide, flagella, and capsule in Campylobacter species. PV of components of these molecules is potentially important during invasion of host tissues, spread within hosts and transmission between hosts. Motility is a critical phenotype that is potentially modulated by PV. Variation in the status of the phase-variable genes has been observed to occur during colonization in chickens and mouse infection models. Interestingly, PV is also involved in bacterial survival of attack by bacteriophages even during chicken colonization. This review aims to explore and discuss observations of PV during model and natural infections by Campylobacter species and how PV may affect strategies for fighting infections by this foodborne pathogen.

Approximately 3–5% of women experience post-traumatic stress disorder following birth; positive experiences that can follow traumatic birth are under-researched. To explore how women experience post-traumatic growth following a traumatic birth. Interpretative Phenomenological Analysis was used to explore experiences of women who self-identified as having found positive benefits through coping with a traumatic birth. Eight women who had birthed in the past five years in the UK were recruited online and interviewed face-to-face. Three superordinate themes were developed: 'The total opposite to what I'd expected' (participants' struggle to understand and integrate their birth experience in the postnatal period); 'I see it a bit differently now' (processes experienced in coming to a place of growth); and 'A much better place' (experienced growth 'outcomes'). Faced with shattered assumptions whereby their birth experiences contrasted with their expectations, participants felt their identities as women and mothers were challenged. In overcoming these challenges, participants described actively striving to cope and make sense of their experience. Multiple factors facilitated this, notably partner support, telling their birth story, acknowledging the impact and developing a compassionate narrative. Although growth was experienced in ways commonly reported by survivors of challenging life events, some aspects appeared pertinent to birth trauma. Widening our understanding of the range of experiences following traumatic birth and making these narratives public may offer hope for some women and families and inform health professionals' education and practice. Further research would be needed before advocating interventions to foster post-traumatic growth. [ABSTRACT FROM AUTHOR]

Our genome is constantly exposed to endogenous and exogenous sources of DNA damage resulting in various alterations of the genetic code. DNA double-strand breaks (DSBs) are considered one of the most cytotoxic lesions. Several types of repair pathways act to repair DNA damage and maintain genome stability. In the canonical DNA damage response (DDR) DSBs are recognized by the sensing kinases Ataxia-telangiectasia mutated (ATM), Ataxia-telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK), which initiate a cascade of kinase-dependent amplification steps known as DSB signaling. Recent evidence suggests that efficient recognition and repair of DSBs relies on the transcription and processing of non-coding (nc)RNA molecules by RNA polymerase II (RNAPII) and the RNA interference (RNAi) factors Drosha and Dicer. Multiple kinases influence the phosphorylation status of both the RNAPII carboxy-terminal domain (CTD) and Dicer in order to regulate RNA-dependent DSBs repair. The importance of kinase signaling and RNA processing in the DDR is highlighted by the regulation of p53-binding protein (53BP1), a key regulator of DSB repair pathway choice between homologous recombination (HR) and non-homologous end joining (NHEJ). Additionally, emerging evidence suggests that RNA metabolic enzymes also play a role in the repair of other types of DNA damage, including the DDR to ultraviolet radiation (UVR). RNAi factors are also substrates for mitogen-activated protein kinase (MAPK) signaling and mediate the turnover of ncRNA during nucleotide excision repair (NER) in response to UVR. Here, we review kinase-dependent phosphorylation events on RNAPII, Drosha and Dicer, and 53BP1 that modulate the key steps of the DDR to DSBs and UVR, suggesting an intimate link between the DDR and RNA metabolism.

Background Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares. Methods Faecal samples were collected weekly from five pregnant mares from 3 weeks pre-foaling to 7 weeks post-foaling. The microbiome data was generated by PCR amplification and sequencing of the V1–V2 regions of the bacterial 16S rRNA genes, while the VOC profile was characterised using headspace solid phase microextraction gas chromatography mass spectrometry. Results The mare faecal microbiota was relatively stable over the periparturient period and most variation was associated with individual mares. A small number of operational taxonomic units were found to be significantly differentially abundant between samples collected before and after foaling. A total of 98 VOCs were identified. The total number of VOCs did not vary significantly between individual mares, weeks of sample collection and feeds available to the mares. Three VOCs (decane, 2-pentylfuran, and oct-2-ene) showed significant increase overtime on linear mixed effects modelling analysis. These results suggest that the mare faecal microbiota is structurally and functionally stable during the periparturient period. The findings also suggest that if changes in the gut microbiota are related to development of colic postpartum, altered risk may be due to inherent differences between individual mares. VOCs offer a cost-effective means of looking at the functional changes in the microbiome and warrant further investigation in mares at risk of colic.