The empty pelvis syndrome: a core data set from the PelvEx collaborative

BACKGROUND

Empty pelvis syndrome (EPS) is a significant source of morbidity following pelvic exenteration (PE), but is undefined. EPS outcome reporting and descriptors of radicality of PE are inconsistent; therefore, the best approaches for prevention are unknown. To facilitate future research into EPS, the aim of this study is to define a measurable core outcome set, core descriptor set and written definition for EPS. Consensus on strategies to mitigate EPS was also explored.

METHOD

Three-stage consensus methodology was used: longlisting with systematic review, healthcare professional event, patient engagement, and Delphi-piloting; shortlisting with two rounds of modified Delphi; and a confirmatory stage using a modified nominal group technique. This included a selection of measurement instruments, and iterative generation of a written EPS definition.

RESULTS

One hundred and three and 119 participants took part in the modified Delphi and consensus meetings, respectively. This encompassed international patient and healthcare professional representation with multidisciplinary input. Seventy statements were longlisted, seven core outcomes (bowel obstruction, enteroperineal fistula, chronic perineal sinus, infected pelvic collection, bowel obstruction, morbidity from reconstruction, re-intervention, and quality of life), and four core descriptors (magnitude of surgery, radiotherapy-induced damage, methods of reconstruction, and changes in volume of pelvic dead space) reached consensus-where applicable, measurement of these outcomes and descriptors was defined. A written definition for EPS was agreed.

CONCLUSIONS

EPS is an area of unmet research and clinical need. This study provides an agreed definition and core data set for EPS to facilitate further research.

Global survival trends for brain tumors, by histology: analysis of individual records for 556,237 adults diagnosed in 59 countries during 2000-2014 (CONCORD-3)

BACKGROUND

Survival is a key metric of the effectiveness of a health system in managing cancer. We set out to provide a comprehensive examination of worldwide variation and trends in survival from brain tumors in adults, by histology.

METHODS

We analyzed individual data for adults (15-99 years) diagnosed with a brain tumor (ICD-O-3 topography code C71) during 2000-2014, regardless of tumor behavior. Data underwent a 3-phase quality control as part of CONCORD-3. We estimated net survival for 11 histology groups, using the unbiased nonparametric Pohar Perme estimator.

RESULTS

The study included 556,237 adults. In 2010-2014, the global range in age-standardized 5-year net survival for the most common sub-types was broad: in the range 20%-38% for diffuse and anaplastic astrocytoma, from 4% to 17% for glioblastoma, and between 32% and 69% for oligodendroglioma. For patients with glioblastoma, the largest gains in survival occurred between 2000-2004 and 2005-2009. These improvements were more noticeable among adults diagnosed aged 40-70 years than among younger adults.

CONCLUSIONS

To the best of our knowledge, this study provides the largest account to date of global trends in population-based survival for brain tumors by histology in adults. We have highlighted remarkable gains in 5-year survival from glioblastoma since 2005, providing large-scale empirical evidence on the uptake of chemoradiation at population level. Worldwide, survival improvements have been extensive, but some countries still lag behind. Our findings may help clinicians involved in national and international tumor pathway boards to promote initiatives aimed at more extensive implementation of clinical guidelines.

The Cost-effectiveness of Watch and Wait for Rectal Cancer

The existing literature suggests with a high degree of certainty that watch and wait is more cost-effective than initial total mesorectal excision. However, it is heavily reliant on poor-quality health-related quality of life data. Furthermore, the cost-effectiveness of organ preservation from a broader societal perspective has not been studied. Finally, the cost-effectiveness of emerging adjuncts to watch and wait for organ preservation, such as contact X-ray brachytherapy, local excision and total neoadjuvant therapy, need to be characterised.

Minimum standards of pelvic exenterative practice: PelvEx Collaborative guideline

This document outlines the important aspects of caring for patients who have been diagnosed with advanced pelvic cancer. It is primarily aimed at those who are establishing a service that adequately caters to this patient group. The relevant literature has been summarized and an attempt made to simplify the approach to management of these complex cases.

Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite

The human gut microbiota resides within a diverse chemical environment challenging our ability to understand the forces shaping this ecosystem. Here, we reveal that fitness of the Bacteroidales, the dominant order of bacteria in the human gut, is an emergent property of glycans and one specific metabolite, butyrate. Distinct sugars serve as strain-variable fitness switches activating context-dependent inhibitory functions of butyrate. Differential fitness effects of butyrate within the Bacteroides are mediated by species-level variation in Acyl-CoA thioesterase activity and nucleotide polymorphisms regulating an Acyl-CoA transferase. Using in vivo multi-omic profiles, we demonstrate Bacteroides fitness in the human gut is associated together, but not independently, with Acyl-CoA transferase expression and butyrate. Our data reveal that each strain of the Bacteroides exists within a unique fitness landscape based on the interaction of chemical components unpredictable by the effect of each part alone mediated by flexibility in the core genome.

711 Effect of Roux-En-Y Gastric Bypass on HbA1c As Well As Number of Medications in Diabetic Patients

Aim

Roux en Y gastric bypass (RYGB) is known to ameliorate Type 2 Diabetes Mellitus (T2DM) in morbidly obese patients. We aimed to determine both the reduction in the glycosylated haemoglobin (HbA1c) and the number of anti-diabetic medications (including insulin) in diabetic patients undergoing RYGB over a five-year period.

Method

We reviewed data of diabetic patients (n = 530) who underwent RYGB from January 2012 – December 2017, including those with a minimum of a 2-year post-operative follow up (n = 47). Preoperatively, BMI, HbA1c and the number of anti-diabetic medications and the duration of T2DM since diagnosis were recorded. These measurements were repeated at the end of the two year follow up.

Results

At the time of enrolment in the bariatric programme, the median BMI was 42.5 (range, 31.7-61.5) kg/m2, mean duration of T2DM was 58 months and median HbA1c was 59 (37-118) mmol/mol. The mean number of anti-diabetic medications taken, including insulin, was 2. At the end of 2-year follow-up, the median BMI was 32 (range, 24-41) kg/m2 and HbA1c was 41(range, 33-91) mmol/mol. 15 patients (31.9%) still required anti-diabetic medication, 12 of whom had a diagnosis of T2DM for 3 years or more at time of enrolment.

Conclusions

RYGB is strongly associated with a resolution of T2DM in morbidly obese patients. In those who were not resolved, the number of anti-diabetic medications taken and HbA1c were reduced. The impact of the surgery is dependent on the duration of T2DM since diagnosis preoperatively.

Combined immunodeficiency due to a mutation in the γ1 subunit of the coat protein I complex

The coat protein I (COPI) complex mediates retrograde trafficking from the Golgi to the endoplasmic reticulum (ER). Five siblings with persistent bacterial and viral infections and defective humoral and cellular immunity had a homozygous p.K652E mutation in the γ1 subunit of COPI (γ1-COP). The mutation disrupts COPI binding to the KDEL receptor and impairs the retrieval of KDEL-bearing chaperones from the Golgi to the ER. Homozygous Copg1K652E mice had increased ER stress in activated T and B cells, poor antibody responses, and normal numbers of T cells that proliferated normally, but underwent increased apoptosis upon activation. Exposure of the mutants to pet store mice caused weight loss, lymphopenia, and defective T cell proliferation that recapitulated the findings in the patients. The ER stress-relieving agent tauroursodeoxycholic acid corrected the immune defects of the mutants and reversed the phenotype they acquired following exposure to pet store mice. This study establishes the role of γ1-COP in the ER retrieval of KDEL-bearing chaperones and thereby the importance of ER homeostasis in adaptive immunity.

Is the Management of Rectal Cancer Using a Watch and Wait Approach Feasible, Safe and Effective in a Publicly Funded General Hospital?

AIMS

Although there is emerging evidence to suggest equivalent oncological outcomes using a watch and wait approach compared with primary total mesorectal excision surgery, there is a paucity of evidence about the safety and efficacy of this approach in routine clinical practice. Here we report the long-term outcomes and quality of life from patients managed with watch and wait following a clinical complete response (cCR) to neoadjuvant therapy.

MATERIALS AND METHODS

Patients with adenocarcinoma of the rectum with cCR following neoadjuvant therapy managed using watch and wait were retrospectively identified. Demographic data, performance status, pretreatment staging information, oncological and surgical outcomes were obtained from routinely collected clinical data. Quality of life was measured by trained clinicians during telephone interviews.

RESULTS

Over a 7-year period, 506 patients were treated for rectal cancer, 276 had neoadjuvant therapy and 72 had a cCR (26.1%). Sixty-three were managed with watch and wait. Thirteen patients had mucosal regrowth. There was no significant difference in the incidence of metastatic disease between the surgical and watch and wait cohorts (P = 0.38). The 13 patients with mucosal regrowth underwent salvage surgery. Eleven of the patients who underwent surgical resection had R0 resections. There was also a statistically and clinically significant improvement in the Functional Assessment of Cancer Therapy - Colorectal (FACT-C) trial outcome index (P = 0.022).

CONCLUSION

This study shows that watch and wait is safe and effective outside of tertiary referral centres. It suggests that an opportunistic cCR is durable and when mucosal regrowth occurs it can be salvaged. Finally, we have shown that quality of life is probably improved if a watch and wait approach is adopted.

Effect of the SARS-CoV-2 pandemic on mortality related to high-risk emergency and major elective surgery

These data show large reductions in both elective and emergency activity that are concerning for unmeasured morbidity and mortality within the community. The risk of mortality following high-risk EGS and major elective surgery during the first wave of the pandemic did not differ when compared with date-matched patient cohorts from 2019. The prevalence of concomitant SARS-CoV-2 infection in this surgical population is low.

Multi-kingdom ecological drivers of microbiota assembly in preterm infants

The gut microbiota of preterm infants develops predictably1-7, with pioneer species colonizing the gut after birth, followed by an ordered succession of microorganisms. The gut microbiota is vital to the health of preterm infants8,9, but the forces that shape these predictable dynamics of microbiome assembly are unknown. The environment, the host and interactions between microorganisms all potentially shape the dynamics of the microbiota, but in such a complex ecosystem, identifying the specific role of any individual factor is challenging10-14. Here we use multi-kingdom absolute abundance quantification, ecological modelling and experimental validation to address this challenge. We quantify the absolute dynamics of bacteria, fungi and archaea in a longitudinal cohort of 178 preterm infants. We uncover microbial blooms and extinctions, and show that there is an inverse correlation between bacterial and fungal loads in the infant gut. We infer computationally and demonstrate experimentally in vitro and in vivo that predictable assembly dynamics may be driven by directed, context-dependent interactions between specific microorganisms. Mirroring the dynamics of macroscopic ecosystems15-17, a late-arriving member of the microbiome, Klebsiella, exploits the pioneer microorganism, Staphylococcus, to gain a foothold within the gut. Notably, we find that interactions between different kingdoms can influence assembly, with a single fungal species-Candida albicans-inhibiting multiple dominant genera of gut bacteria. Our work reveals the centrality of simple microbe-microbe interactions in shaping host-associated microbiota, which is critical both for our understanding of microbiota ecology and for targeted microbiota interventions.

Ecological rules for the assembly of microbiome communities

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome—with analogies to the mutational maps underlying fitness landscapes in evolutionary biology. Building these “assembly maps” reveals a tradeoff at the heart of the assembly process. Ecological dependencies between members of the microbiota make assembly predictable—and can provide metabolic benefits to the host—but these dependencies may also create barriers to assembly. This effect occurs because interdependent species can fail to establish when each relies on the other to colonize first. We support our predictions with published data from the assembly of the preterm infant microbiota, where we find that ecological dependence is associated with a predictable order of arrival. Our models also suggest that hosts can overcome barriers to assembly via mechanisms that either promote the uptake of multiple symbiont species in one step or feed early colonizers. This predicted importance of host feeding is supported by published data on the impacts of breast milk in the assembly of the human microbiome. We conclude that both microbe to microbe and host to microbe interactions are important for the trajectory of microbiome assembly.

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation, but what determines the success of the assembly process remains poorly understood. This study develops ecological theory that reveals the rules underlying the assembly of such host-associated microbiota.

Mycobacterium tuberculosis 6C sRNA binds multiple mRNA targets via C-rich loops independent of RNA chaperones

Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-depth study of 6C sRNA of Mycobacterium tuberculosis, which is conserved among high GC Gram-positive bacteria. Forty-seven genes were identified as possible direct targets of 6C sRNA and 15 of them were validated using an in vivo translational lacZ fusion system. We found that 6C sRNA plays a pleotropic role and regulates genes involved in various cellular processes, including DNA replication and protein secretion. Mapping the interactions of 6C sRNA with mRNA targets panD and dnaB revealed that the C-rich loops of 6C sRNA act as direct binding sites to mRNA targets. Unlike in Gram-negative bacteria where RNA binding proteins Hfq and ProQ are required, the interactions of 6C sRNA with mRNAs appear to be independent of RNA chaperones. Our findings suggest that the multiple G–C pairings between single stranded regions are sufficient to establish stable interactions between 6C sRNA and mRNA targets, providing a mechanism for sRNAs in high GC Gram-positive bacteria.

Contact X-ray Brachytherapy as an Adjunct to a Watch and Wait Approach is an Affordable Alternative to Standard Surgical Management of Rectal Cancer for Patients with a Partial Clinical Response to Chemoradiotherapy

AIMS

Emerging evidence suggests that contact X-ray brachytherapy (CXB) may increase the clinical complete response rate and durability when administered after standard chemoradiotherapy in patients with rectal cancer. The addition of CXB in partial responders is therefore probably cost-effective. The affordability of widening access to CXB in the UK, however, has not been evaluated.

MATERIALS AND METHODS

Decision analytical modelling with Monte Carlo simulation was used to evaluate long-term costs for the management of patients with rectal cancers who were given a CXB boost when a clinical complete response was not initially achieved following chemoradiotherapy in order to facilitate a watch and wait approach. A third-party payer (National Health Service) perspective was adopted, probabilistic sensitivity analysis was carried out and a scenario analysis was performed to investigate the effect of the number of referral centres and number of patients treated with CXB.

RESULTS

We estimate that 818 (95% confidence interval 628-1021) patients per year are eligible for CXB as an adjunct to a watch and wait approach in England and Wales. As this management is less costly than surgical management for each individual patient, the more patients treated, the more affordable the technology. Even if as few as 125 patients are treated nationally in 15 centres, the cost of implementing this technology would be less than £4 million. If the average number of patients treated in each centre is 30, this technology would be cost saving within 5 years.

CONCLUSIONS

The cost of CXB is not prohibitive according to the National Institute for Health and Care Excellence threshold for implementation of new technology and may even be cost saving within 5 years compared with standard surgical management, depending on the uptake of the technology and the number of referral centres.

Priming in a permissive type I-C CRISPR-Cas system reveals distinct dynamics of spacer acquisition and loss

CRISPR-Cas is a bacterial and archaeal adaptive immune system that uses short, invader-derived sequences termed spacers to target invasive nucleic acids. Upon recognition of previously encountered invaders, the system can stimulate secondary spacer acquisitions, a process known as primed adaptation. Previous studies of primed adaptation have been complicated by intrinsically high interference efficiency of most systems against bona fide targets. As such, most primed adaptation to date has been studied within the context of imperfect sequence complementarity between spacers and targets. Here, we take advantage of a native type I-C CRISPR-Cas system in Legionella pneumophila that displays robust primed adaptation even within the context of a perfectly matched target. Using next-generation sequencing to survey acquired spacers, we observe strand bias and positional preference that are consistent with a 3'-5' translocation of the adaptation machinery. We show that spacer acquisition happens in a wide range of frequencies across the plasmid, including a remarkable hotspot that predominates irrespective of the priming strand. We systematically characterize protospacer sequence constraints in both adaptation and interference and reveal extensive flexibilities regarding the protospacer adjacent motif in both processes. Lastly, in a strain with a genetically truncated CRISPR array, we observe increased interference efficiency, which, when coupled with forced maintenance of a targeted plasmid, provides a useful experimental system to study spacer loss. Based on these observations, we propose that the Legionella pneumophila type I-C system represents a powerful model to study primed adaptation and the interplay between CRISPR interference and adaptation.

An evaluation of cause-of-death trends from recent decades based on registered deaths in Turkey

OBJECTIVES

Although cause-of-death analyses are very important to define public health policy priorities and to evaluate health programs, there is very limited knowledge about mortality profiles and trends in Turkey. The aim of this study was to measure the trends in mortality within three broad cause-of-death groups and their distribution by age groups and gender and to describe the changes of leading causes of death between 1980 and 2013 in Turkey.

STUDY DESIGN

Descriptive study.

METHODS

In the study, data on the number of deaths by year, gender, age and cause was obtained from the Turkish Statistical Institute. The causes of death were classified as group I: communicable, maternal, perinatal, and nutritional conditions; group II: non-communicable diseases (NCDs); and group III: injuries. Unknown or ill-defined causes of death were distributed within group I and group II. The percentage distribution of the cause-of-death groups by gender and age groups between 1980 and 2013 was identified. Age-standardized mortality rates (ASMRs) per 100,000 of broad causes-of-death groups were calculated using European Standard Population 1976 between 1980 and 2008. Changes in mortality rates per hundred were calculated using the formula ([the rate of last year of the period-the rate of the first year of the period]/the rate of the first year of the period). Gender and age-specific data were analyzed using the Joinpoint software to examine trends and significant changes in trends of mortality rates.

RESULTS

Crude death rates for group I, group II, and group III were 157.3, 147.2, and 21.4 per 100,000 in 1980 and 35.3, 377.5, and 15.8 in 2008 for males; 161.8, 120.2, and 5.8 in 1980 and 38.6, 318.4, and 6.4 in 2008 for females, respectively. ASMRs for group I, group II, and group III were 146.3, 394.3, and 29.3 per 100,000 in 1980 and 49.7, 723.6, and 18.8 in 2008 for males; 138.0, 291.5, and 7.6 per 100,000 in 1980 and 47.7, 478.8, and 7.2 in 2008 for females, respectively. The mortality rates of group I for almost all age groups particularly below 5 years of age decreased significantly.

CONCLUSION

This study indicates that Turkey is at an advanced stage in the epidemiological transition, with the majority of the causes of death from NCDs. Considering the regional differences, it is necessary to carry out studies on the specific details of epidemiological transition and the social determinants of deaths in Turkey.

Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells

Replication stress is a characteristic feature of cancer cells, which is resulted from sustained proliferative signaling induced by activation of oncogenes or loss of tumor suppressors. In cancer cells, oncogene-induced replication stress manifests as replication-associated lesions, predominantly double-strand DNA breaks (DSBs). An essential mechanism utilized by cells to repair replication-associated DSBs is homologous recombination (HR). In order to overcome replication stress and survive, cancer cells often require enhanced HR repair capacity. Therefore, the key link between HR repair and cellular tolerance to replication-associated DSBs provides us with a mechanistic rationale for exploiting synthetic lethality between HR repair inhibition and replication stress. DNA2 nuclease is an evolutionarily conserved essential enzyme in replication and HR repair. Here we demonstrate that DNA2 is overexpressed in pancreatic cancers, one of the deadliest and more aggressive forms of human cancers, where mutations in the KRAS are present in 90–95% of cases. In addition, depletion of DNA2 significantly reduces pancreatic cancer cell survival and xenograft tumor growth, suggesting the therapeutic potential of DNA2 inhibition. Finally, we develop a robust high-throughput biochemistry assay to screen for inhibitors of the DNA2 nuclease activity. The top inhibitors were shown to be efficacious against both yeast Dna2 and human DNA2. Treatment of cancer cells with DNA2 inhibitors recapitulates phenotypes observed upon DNA2 depletion, including decreased DNA double strand break end resection and attenuation of HR repair. Similar to genetic ablation of DNA2, chemical inhibition of DNA2 selectively attenuates the growth of various cancer cells with oncogene-induced replication stress. Taken together, our findings open a new avenue to develop a new class of anticancer drugs by targeting druggable nuclease DNA2. We propose DNA2 inhibition as new strategy in cancer therapy by targeting replication stress, a molecular property of cancer cells that is acquired as a result of oncogene activation instead of targeting currently undruggable oncoprotein itself such as KRAS.

Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila

Pathogens deliver complex arsenals of translocated effector proteins to host cells during infection, but the extent to which these proteins are regulated once inside the eukaryotic cell remains poorly defined. Among all bacterial pathogens, Legionella pneumophila maintains the largest known set of translocated substrates, delivering over 300 proteins to the host cell via its Type IVB, Icm/Dot translocation system. Backed by a few notable examples of effector–effector regulation in L. pneumophila, we sought to define the extent of this phenomenon through a systematic analysis of effector–effector functional interaction. We used Saccharomyces cerevisiae, an established proxy for the eukaryotic host, to query > 108,000 pairwise genetic interactions between two compatible expression libraries of ~330 L. pneumophila‐translocated substrates. While capturing all known examples of effector–effector suppression, we identify fourteen novel translocated substrates that suppress the activity of other bacterial effectors and one pair with synergistic activities. In at least nine instances, this regulation is direct—a hallmark of an emerging class of proteins called metaeffectors, or “effectors of effectors”. Through detailed structural and functional analysis, we show that metaeffector activity derives from a diverse range of mechanisms, shapes evolution, and can be used to reveal important aspects of each cognate effector's function. Metaeffectors, along with other, indirect, forms of effector–effector modulation, may be a common feature of many intracellular pathogens—with unrealized potential to inform our understanding of how pathogens regulate their interactions with the host cell.

Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen

Clustered regularly interspaced short palindromic repeats with CRISPR‐associated gene (CRISPR‐Cas) systems are widely recognized as critical genome defense systems that protect microbes from external threats such as bacteriophage infection. Several isolates of the intracellular pathogen Legionella pneumophila possess multiple CRISPR‐Cas systems (type I‐C, type I‐F and type II‐B), yet the targets of these systems remain unknown. With the recent observation that at least one of these systems (II‐B) plays a non‐canonical role in supporting intracellular replication, the possibility remained that these systems are vestigial genome defense systems co‐opted for other purposes. Our data indicate that this is not the case. Using an established plasmid transformation assay, we demonstrate that type I‐C, I‐F and II‐B CRISPR‐Cas provide protection against spacer targets. We observe efficient laboratory acquisition of new spacers under ‘priming’ conditions, in which initially incomplete target elimination leads to the generation of new spacers and ultimate loss of the invasive DNA. Critically, we identify the first known target of L. pneumophila CRISPR‐Cas: a 30 kb episome of unknown function whose interbacterial transfer is guarded against by CRISPR‐Cas. We provide evidence that the element can subvert CRISPR‐Cas by mutating its targeted sequences – but that primed spacer acquisition may limit this mechanism of escape. Rather than generally impinging on bacterial fitness, this element drives a host specialization event – with improved fitness in Acanthamoeba but a reduced ability to replicate in other hosts and conditions. These observations add to a growing body of evidence that host range restriction can serve as an existential threat to L. pneumophila in the wild.

Femoral cortical index: an indicator of poor bone quality in patient with hip fracture

BACKGROUND

Osteoporosis is a common disease in elderly, characterized by poor bone quality as a result of alterations affecting trabecular bone. However, recent studies have described also an important role of alterations of cortical bone in the physiopathology of osteoporosis. Although dual-energy X-ray absorptiometry (DXA) is a valid method to assess bone mineral density, in the presence of comorbidities real bone fragility is unable to be evaluated. The number of hip fractures is rising, especially in people over 85 years old.

AIMS

The aim is to evaluate an alternative method so that it can indicate fracture risk, independent of bone mineral density (BMD). Femoral cortical index (FCI) assesses cortical bone stock using femur X-ray.

METHODS

A retrospective study has been conducted on 152 patients with hip fragility fractures. FCI has been calculated on fractured femur and on the opposite side. The presence of comorbidities, osteoporosis risk factors, vitamin D levels, and BMD have been analyzed for each patient.

RESULTS

Average values of FCI have been 0.42 for fractured femurs and 0.48 at the opposite side with a statistically significant difference (p = 0.002). Patients with severe hypovitaminosis D had a minor FCI compared to those with moderate deficiency (0.41 vs. 0.46, p < 0.011). 42 patients (27.6%) with osteopenic or normal BMD have presented low values of FCI.

DISCUSSION AND CONCLUSION

A significant correlation among low values of FCI, comorbidities, severe hypovitaminosis D. and BMD in patients with hip fractures has been found. FCI could be a useful tool to evaluate bone fragility and to predict fracture risk even in the normal and osteopenic BMD patients.

Silencing by H-NS potentiated the evolution of Salmonella

The bacterial H-NS protein silences expression from sequences with higher AT-content than the host genome and is believed to buffer the fitness consequences associated with foreign gene acquisition. Loss of H-NS results in severe growth defects in Salmonella, but the underlying reasons were unclear. An experimental evolution approach was employed to determine which secondary mutations could compensate for the loss of H-NS in Salmonella. Six independently derived S. Typhimurium hns mutant strains were serially passaged for 300 generations prior to whole genome sequencing. Growth rates of all lineages dramatically improved during the course of the experiment. Each of the hns mutant lineages acquired missense mutations in the gene encoding the H-NS paralog StpA encoding a poorly understood H-NS paralog, while 5 of the mutant lineages acquired deletions in the genes encoding the Salmonella Pathogenicity Island-1 (SPI-1) Type 3 secretion system critical to invoke inflammation. We further demonstrate that SPI-1 misregulation is a primary contributor to the decreased fitness in Salmonella hns mutants. Three of the lineages acquired additional loss of function mutations in the PhoPQ virulence regulatory system. Similarly passaged wild type Salmonella lineages did not acquire these mutations. The stpA missense mutations arose in the oligomerization domain and generated proteins that could compensate for the loss of H-NS to varying degrees. StpA variants most able to functionally substitute for H-NS displayed altered DNA binding and oligomerization properties that resembled those of H-NS. These findings indicate that H-NS was central to the evolution of the Salmonellae by buffering the negative fitness consequences caused by the secretion system that is the defining characteristic of the species.

Selective hydrophilic modification of Parylene C films: a new approach to cell micro-patterning for synthetic biology applications

We demonstrate a simple, accurate and versatile method to manipulate Parylene C, a material widely known for its high biocompatibility, and transform it to a substrate that can effectively control the cellular microenvironment and consequently affect the morphology and function of the cells in vitro. The Parylene C scaffolds are fabricated by selectively increasing the material's surface water affinity through lithography and oxygen plasma treatment, providing free bonds for attachment of hydrophilic biomolecules. The micro-engineered constructs were tested as culture scaffolds for rat ventricular fibroblasts and neonatal myocytes (NRVM), toward modeling the unique anisotropic architecture of native cardiac tissue. The scaffolds induced the patterning of extracellular matrix compounds and therefore of the cells, which demonstrated substantial alignment compared to typical unstructured cultures. Ca(2+) cycling properties of the NRVM measured at rates of stimulation 0.5-2 Hz were significantly modified with a shorter time to peak and time to 90% decay, and a larger fluorescence amplitude (p < 0.001). The proposed technique is compatible with standard cell culturing protocols and exhibits long-term pattern durability. Moreover, it allows the integration of monitoring modalities into the micro-engineered substrates for a comprehensive interrogation of physiological parameters.

Phylogenetic reconstruction of the Legionella pneumophila Philadelphia-1 laboratory strains through comparative genomics

Over 20 years ago, two groups independently domesticated Legionella pneumophila from a clinical isolate of bacteria collected during the first recognized outbreak of Legionnaires' disease (at the 1976 American Legion's convention in Philadelphia). These two laboratory strains, JR32 and Lp01, along with their derivatives, have been disseminated to a number of laboratories around the world and form the cornerstone of much of the research conducted on this important pathogen to date. Nevertheless, no exhaustive examination of the genetic distance between these strains and their clinical progenitor has been performed thus far. Such information is of paramount importance for making sense of several phenotypic differences observed between these strains. As environmental replication of L. pneumophila is thought to exclusively occur within natural protozoan hosts, retrospective analysis of the domestication and axenic culture of the Philadelphia-1 progenitor strain by two independent groups also provides an excellent opportunity to uncover evidence of adaptation to the laboratory environment. To reconstruct the phylogenetic relationships between the common laboratory strains of L. pneumophila Philadelphia-1 and their clinical ancestor, we performed whole-genome Illumina resequencing of the two founders of each laboratory lineage: JR32 and Lp01. As expected from earlier, targeted studies, Lp01 and JR32 contain large deletions in the lvh and tra regions, respectively. By sequencing additional strains derived from Lp01 (Lp02 and Lp03), we retraced the phylogeny of these strains relative to their reported ancestor, thereby reconstructing the evolutionary dynamics of each laboratory lineage from genomic data.