Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing.

Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.

Outcomes of community-based hepatitis C treatment by general practitioners and nurses in Australia through remote specialist consultation.

BACKGROUND: A unique model of care was adopted in Australia following introduction of universal subsidised direct-acting antiviral (DAA) access in 2016 in order to encourage rapid scale-up of treatment. Community-based medical practitioners and integrated hepatitis nurses initiated DAA treatment with remote hepatitis specialist approval of the planned treatment without physical review. AIMS: To evaluate outcomes of community-based treatment of hepatitis C virus (HCV) through this remote consultation process in the first 12 months of this model of care. METHODS: A retrospective chart review of patients undergoing community-based HCV treatment from general practitioners and integrated hepatitis nurse consultants through the remote consultation model in three state jurisdictions in Australia from 1 March 2016 to 28 February 2017. RESULTS: Sustained virological response at 12 weeks (SVR12) was confirmed in 383 (65.1%) of 588 subjects intended for treatment with a median follow-up time of 12 months (interquartile range 9-14 months). The SVR12 test was not performed in 159 (27.0%) of 588 and 307 (52.2%) of 588 did not have liver biochemistry rechecked following treatment. Subjects who completed follow up exhibited high SVR12 rates (383/392; 97.7%). Nurse-led treatment was associated with higher confirmation of SVR12 (73.7% vs 62.4%; P = 0.01) and liver biochemistry testing post treatment (57.5% vs 45.0%; P = 0.01). CONCLUSIONS: Community-based management of HCV through remote specialist consultation may be an effective model of care. Failure to check SVR12, recheck liver biochemistry and appropriate surveillance in patients with cirrhosis may emerge as significant issues requiring further support, education and refinement of the model to maximise effectiveness of future elimination efforts.

Hepatitis C virus infection in Australian psychiatric inpatients: A multicenter study of seroprevalence, risk factors and treatment experience.

Screening and treatment for hepatitis C virus (HCV) infection were not prioritised in psychiatric patients due to adverse neuropsychiatric effects of interferon therapy despite reports of high prevalence. However, with the safe new antiviral drugs, HCV eradication has become a reality in these patients. The aim of this study was to report HCV seroprevalence, risk factors and treatment model in an Australian cohort. This prospective study involved patients admitted to four inpatient psychiatric units, from December 2016 to December 2017. After pretest counselling and consent, HCV testing was done; information on risk factors collected. A total of 260 patients (70% male), median age 44 years (IQR 24), were studied. The HCV seroprevalence was 10.8% (28/260) with 95% CI 7-15. Independent predictors of HCV positivity were injection drug use (P < 0.001, OR 44.05, 95% CI 7.9-245.5), exposure to custodial stay (P = 0.011, OR 7.34, 95% CI 1.6-33.9) and age (P = 0.011, OR 1.09, 95% CI 1.02-1.16). Eight of the 16 HCV RNA-positive patients were treated. Hepatitis nurses liaised with community mental health teams for treatment initiation and follow-up under supervision of hepatologists. Seven patients achieved sustained viral response, one achieved end of treatment response. The remaining eight patients were difficult to engage with. In conclusion, HCV prevalence was high in our cohort of psychiatric inpatients. Although treatment uptake was achieved only in 50% patients, it was successfully completed in all, with innovative models of care. These findings highlight the need to integrate HCV screening with treatment linkage in psychiatry practice.

Unique Function of the Bacterial Chromosome Segregation Machinery in Apically Growing Streptomyces - Targeting the Chromosome to New Hyphal Tubes and its Anchorage at the Tips.

The coordination of chromosome segregation with cell growth is fundamental to the proliferation of any organism. In most unicellular bacteria, chromosome segregation is strictly coordinated with cell division and involves ParA that moves the ParB nucleoprotein complexes bi- or unidirectionally toward the cell pole(s). However, the chromosome organization in multiploid, apically extending and branching Streptomyces hyphae challenges the known mechanisms of bacterial chromosome segregation. The complex Streptomyces life cycle involves two stages: vegetative growth and sporulation. In the latter stage, multiple cell divisions accompanied by chromosome compaction and ParAB assisted segregation turn multigenomic hyphal cell into a chain of unigenomic spores. However, the requirement for active chromosome segregation is unclear in the absence of canonical cell division during vegetative growth except in the process of branch formation. The mechanism by which chromosomes are targeted to new hyphae in streptomycete vegetative growth has remained unknown until now. Here, we address the question of whether active chromosome segregation occurs at this stage. Applied for the first time in Streptomyces, labelling of the chromosomal replication initiation region (oriC) and time-lapse microscopy, revealed that in vegetative hyphae every copy of the chromosome is complexed with ParB, whereas ParA, through interaction with the apical protein complex (polarisome), tightly anchors only one chromosome at the hyphal tip. The anchor is maintained during replication, when ParA captures one of the daughter oriCs. During spore germination and branching, ParA targets one of the multiple chromosomal copies to the new hyphal tip, enabling efficient elongation of hyphal tube. Thus, our studies reveal a novel role for ParAB proteins during hyphal tip establishment and extension.

Spatial variation in risk for tick-borne diseases in residential areas of Dutchess County, New York.

Although human exposure to the ticks that transmit Lyme-disease bacteria is widely considered to occur around people's homes, most studies of variation in tick abundance and infection are undertaken outside residential areas. Consequently, the patterns of variation in risk of human exposure to tick-borne infections in these human-dominated landscapes are poorly understood. Here, we report the results of four years of sampling for tick abundance, tick infection, tick encounters, and tick-borne disease reports on residential properties nested within six neighborhoods in Dutchess County, New York, USA, an area of high incidence for Lyme and other tick-borne diseases. All properties were within neighborhoods that had been randomly assigned as placebo controls in The Tick Project; hence, none were treated to reduce tick abundance during the period of investigation, providing a unique dataset of natural variation within and between neighborhoods. We estimated the abundance of host-seeking blacklegged ticks (Ixodes scapularis) in three types of habitats on residential properties-forests, lawns, and gardens. In forest and lawn habitats, some neighborhoods had consistently higher tick abundance. Properties within neighborhoods also varied consistently between years, suggesting hot spots and cold spots occurring at a small (~ 1-hectare) spatial scale. Across neighborhoods, the abundance of nymphal ticks was explained by neither the amount of forest in that neighborhood, nor by the degree of forest fragmentation. The proportion of ticks infected with three common tick-borne pathogens did not differ significantly between neighborhoods. We observed no effect of tick abundance on human encounters with ticks, nor on either human or pet cases of tick-borne diseases. However, the number of encounters between ticks and outdoor pets in a neighborhood was negatively correlated with the abundance of questing ticks in that neighborhood. Our results reinforce the need to understand how human behavior and neglected ecological factors affect variation in human encounters with ticks and cases of tick-borne disease in residential settings.

Finding the missing and unknown: Novel educational approaches to warming up cold cases.

In recent years, students in police academies and higher education institutions around the world have worked together to analyse cold cases including long-term missing persons cases in collaboration with investigators and prosecutors. In 2020, three European organisations, the Police Expert Network on Missing Persons (PEN-MP), AMBER Alert Europe and Locate International, succeeded in connecting these educational organisations enabling them to work collectively on cases and conduct cold case analyses (CCA) across international borders. The International Cold Case Analysis Project (ICCAP) learning objectives were to 1) collect the necessary information about the victim, 2) reconstruct the crime, and 3) investigate trace control. In a learning objective-based evaluation using Computer-Assisted Web Interviewing, 76 participating students from the German and International ICCAP teams were asked to complete a pre- and post-review questionnaire to self-assess their personal competence development. Participants reported significant increases in competence in all evaluated areas, thus demonstrating that authentic and relevant collaborations can enrich the learning environment, promote the use of professional skills, and provide significant knowledge exchange opportunities between academia and industry. Drawing on case studies of cold case missing persons' investigations and unidentified found remains, this article shares how university academics, students and community volunteers can work together nationally and internationally to find out what has happened to missing people and how we can more effectively identify the previously unidentified. In so doing, we share the expertise required to progress these cold cases and provide recommendations to support other institutions and organisations in adopting this innovative approach.

FGF1 and insulin control lipolysis by convergent pathways.

Inexorable increases in insulin resistance, lipolysis, and hepatic glucose production (HGP) are hallmarks of type 2 diabetes. Previously, we showed that peripheral delivery of exogenous fibroblast growth factor 1 (FGF1) has robust anti-diabetic effects mediated by the adipose FGF receptor (FGFR) 1. However, its mechanism of action is not known. Here, we report that FGF1 acutely lowers HGP by suppressing adipose lipolysis. On a molecular level, FGF1 inhibits the cAMP-protein kinase A axis by activating phosphodiesterase 4D (PDE4D), which separates it mechanistically from the inhibitory actions of insulin via PDE3B. We identify Ser44 as an FGF1-induced regulatory phosphorylation site in PDE4D that is modulated by the feed-fast cycle. These findings establish the FGF1/PDE4 pathway as an alternate regulator of the adipose-HGP axis and identify FGF1 as an unrecognized regulator of fatty acid homeostasis.

Replisome trafficking in growing vegetative hyphae of Streptomyces coelicolor A3(2).

We observed movies of replisome trafficking during Streptomyces coelicolor growth. A replisome(s) in the spore served as a replication center(s) until hyphae reached a certain length, when a tip-proximal replisome formed and moved at a fixed distance behind the tip at a speed equivalent to the extension rate of the tip.

Cost effectiveness of treatment models of care for hepatitis C: the South Australian state-wide experience.

AIM: The objective was to study the long-term (lifetime) cost effectiveness of four different hepatitis C virus (HCV) treatment models of care (MOC) with directly acting antiviral drugs. METHODS: A cohort Markov model-based probabilistic cost-effectiveness analysis (CEA) was undertaken extrapolating to up to 30 years from cost and outcome data collected from a primary study involving a real-life Australian cohort. In this study, noncirrhotic patients treated for HCV from 1 March 2016 to 28 February 2017 at four major public hospitals and liaising sites in South Australia were studied retrospectively. The MOC were classified depending on the person providing patient workup, treatment and monitoring into MOC1 (specialist), MOC2 (mixed specialist and hepatitis nurse), MOC3 (hepatitis nurse) and MOC4 (general practitioner, GP). Incremental costs were estimated from the Medicare perspective. Incremental outcomes were estimated based on the quality-adjusted life years (QALY) gained by achieving a sustained virological response. A cost-effectiveness threshold of Australian dollar 50 000 per QALY gained, the implicit criterion used for assessing the cost-effectiveness of new pharmaceuticals and medical services in Australia was assumed. Net monetary benefit (NMB) estimates based on this threshold were calculated. RESULTS: A total of 1373 patients, 64% males, mean age 50 (SD ±11) years, were studied. In the CEA, MOC4 and MOC2 clearly dominated MOC1 over 30 years with lower costs and higher QALYs. Similarly, NMB was the highest in MOC4, followed by MOC2. CONCLUSION: Decentralized care using GP and mixed consultant nurse models were cost-effective ways of promoting HCV treatment uptake in the setting of unrestricted access to new antivirals.

Time-lapse microscopy of Streptomyces coelicolor growth and sporulation.

Bacteria from the genus Streptomyces are among the most complex of all prokaryotes; not only do they grow as a complex mycelium, they also differentiate to form aerial hyphae before developing further to form spore chains. This developmental heterogeneity of streptomycete microcolonies makes studying the dynamic processes that contribute to growth and development a challenging procedure. As a result, in order to study the mechanisms that underpin streptomycete growth, we have developed a system for studying hyphal extension, protein trafficking, and sporulation by time-lapse microscopy. Through the use of time-lapse microscopy we have demonstrated that Streptomyces coelicolor germ tubes undergo a temporary arrest in their growth when in close proximity to sibling extension sites. Following germination, in this system, hyphae extended at a rate of approximately 20 microm h(-1), which was not significantly different from the rate at which the apical ring of the cytokinetic protein FtsZ progressed along extending hyphae through a spiraling movement. Although we were able to generate movies for streptomycete sporulation, we were unable to do so for either the erection of aerial hyphae or the early stages of sporulation. Despite this, it was possible to demonstrate an arrest of aerial hyphal development that we suggest is through the depolymerization of FtsZ-enhanced green fluorescent protein (GFP). Consequently, the imaging system reported here provides a system that allows the dynamic movement of GFP-tagged proteins involved in growth and development of S. coelicolor to be tracked and their role in cytokinesis to be characterized during the streptomycete life cycle.

Engineering primary metabolic pathways of industrial micro-organisms.

Metabolic engineering is a powerful tool for the optimisation and the introduction of new cellular processes. This is mostly done by genetic engineering. Since the introduction of this multidisciplinary approach, the success stories keep accumulating. The primary metabolism of industrial micro-organisms has been studied for long time and most biochemical pathways and reaction networks have been elucidated. This large pool of biochemical information, together with data from proteomics, metabolomics and genomics underpins the strategies for design of experiments and choice of targets for manipulation by metabolic engineers. These targets are often located in the primary metabolic pathways, such as glycolysis, pentose phosphate pathway, the TCA cycle and amino acid biosynthesis and mostly at major branch points within these pathways. This paper describes approaches taken for metabolic engineering of these pathways in bacteria, yeast and filamentous fungi.

Streptomycin production by Streptomyces griseus can be modulated by a mechanism not associated with change in the adpA component of the A-factor cascade.

In Streptomyces coelicolor, AtrA is an activator of transcription of the actinorhodin cluster-situated regulator gene actII-ORF4. In previous work, we showed that S. coelicolor AtrA binds in vitro to the promoter of S. griseus strR, the streptomycin cluster-situated regulator. We show here that S. griseus carries a single close homologue of atrA and that expression of S. coelicolor AtrA in S. griseus causes a DNA binding-dependent reduction in streptomycin production and in the mRNA levels of strR and genes of streptomycin biosynthesis. However, there is no effect on the level of the mRNA of adpA, which is the only transcription factor that has so far been characterised for strR. The adpA gene is directly regulated by ArpA, the receptor protein for the gamma-butyrolactone signalling molecule A-factor. Therefore, to our knowledge, our results provide the first in vivo evidence that A-factor-ArpA-AdpA-StrR regulatory cascade represents only part of the full complexity of regulation of streptomycin biosynthesis in S. griseus. The potential biotechnological application of our findings is discussed.

Risk factors and associations for the diagnosis of sexually transmitted infections in Aboriginal women presenting to the Alice Springs Hospital emergency department.

OBJECTIVE: To identify risk factors and associations for sexually transmitted infections (STI) in young Aboriginal women presenting to an ED for non-genitourinary reasons, in order to better target opportunistic screening in this group. To determine the prevalence of chlamydia and gonorrhoea in women presenting to the Alice Springs Hospital ED. METHODS: A cross-sectional study involving STI screening and participant interview between January 2007 and September 2007 was used. The participants were a convenience sample of Aboriginal women aged 16-35 years presenting to the Alice Springs Hospital ED for non-genitourinary reasons. The main outcome measures were the prevalence of gonorrhoea and chlamydia and significant associations for STI. RESULTS: A total of 213 women were included in the study. The prevalence rates of women screened were 8.9% for chlamydia, 9.4% for gonorrhoea and 16.0% for gonorrhoea or chlamydia. Identified objective associations for positive STI diagnosis included presenting with an injury due to an assault (odds ratio [OR], 3.56), self-reported past history of an STI (OR, 2.53) and leucocytes on urinalysis (OR, 2.19). CONCLUSION: The prevalence of STI is high in young Aboriginal women presenting to Alice Springs Hospital ED. Screening is acceptable to these patients using low vaginal swabs, and may be targeted at those women with the identified associations. The results of the present study may have relevance to other hospital ED in areas with a high prevalence of STI. A prospective study is needed to confirm these findings.

The genome of Streptomyces rimosus subsp. rimosus shows a novel structure compared to other Streptomyces using DNA/DNA microarray analysis.

DNA/DNA genome microarray analysis together with genome sequencing suggests that the genome of members of the genus Streptomyces would seem to have a common structure including a linear genomic structure, a core of common syntenous Actinomycete genes, the presence of species specific terminal regions and two intermediate group of syntenous genes that seem to be genus specific. We analyzed Streptomyces species using DNA/DNA microarray comparative genome analysis. Only Streptomyces rimosus failed to give a congruent genome pattern for the genes found in Streptomyces coelicolor. We expanded the analysis to include a number of strains related to the type strain of S. rimosus and obtained a similar divergence from the main body of Streptomyces species. These strains showed very close identity to the original strain with no gene deletion or duplication detected. The 16S rRNA sequences of these S. rimosus strains were confirmed as very similar to the S. rimosus sequences available from the Ribosomal Database Project. When the SSU ribosomal RNA phylogeny of S. rimosus is analyzed, the species is positioned at the edge of the Streptomyces clade. We conclude that S. rimosus represents a distinct evolutionary lineage making the species a worthy possibility for genome sequencing.