bluuebunny/crossref_metadata_2025 huggingface dataset:
Immediate Two-Stage Prosthetic Breast Reconstruction Failure: Radiation Is Not the Only Culprit
Authors: Lam Thomas C. , Borotkanics Robert , Hsieh Frank , Salinas James , Boyages John
Published: May 2018

Background:

Immediate prosthetic breast reconstruction produces a satisfactory aesthetic result with high levels of patient satisfaction. However, with the broader indication for postmastectomy adjuvant radiation therapy, many patients are advised against immediate breast reconstruction because of concerns of implant loss and infection, particularly as most patients also require chemotherapy. This retrospective cohort study examines outcomes for patients who underwent immediate two-stage prosthetic breast reconstruction after mastectomy with or without adjuvant chemotherapy or radiotherapy.

Methods:

Between 1998 and 2010, 452 patients undergoing immediate two-stage prosthetic breast reconstruction involving a total of 562 breasts were included in this study. Stage 1 was defined as insertion of the temporary expander, and stage 2 was defined as insertion of the final silicone implant. Postoperative adjuvant radiotherapy was recommended with a tissue expander in situ for 114 patients. Complications, including loss of prosthesis, seroma, and infection, were recorded and analyzed. Cosmetic result was assessed using a four-point scale.

Results:

Postoperative prosthesis loss was 2.7 percent, 5.3 percent for patients undergoing adjuvant chemotherapy and increasing to 11.3 percent for patients receiving chemotherapy plus radiotherapy. Chemotherapy and radiotherapy independently were the main, statistically significant risk factors for expander or implant loss [incidence rate ratio, 13.85 (p = 0.012) and 2.23 (p = 0.027), respectively]. Prosthesis loss for patients undergoing combination chemotherapy plus radiotherapy was also significant [incidence rate ratio, 4.791 (p < 0.001)].

Conclusions:

These findings serve to better inform patients on risk in weighing treatment options. Postmastectomy radiation therapy doubles the risk of prosthesis loss over and above adjuvant chemotherapy but is an acceptable option following immediate two-stage prosthetic breast reconstruction in a multidisciplinary setting.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Relationship between Tamoxifen and the Absorption of Subfascial Autologous Fat Grafts
Authors: Silva Alfredo B. D. , Haupenthal Felipe , Morais André D. , Ascenço Adriana S. K. , Sebastião Ana P. M. , Cavalcanti Manoel A. R. , Freitas Renato S.
Published: May 2018

Background:

In the lipofilling procedures used in breast reconstruction, there is an unpredictability in the rate of reabsorption of the grafted fat. The objective of this study was to analyze the effect of tamoxifen, a medication commonly prescribed for patients with breast cancer, as a possible alternative to reduce the rate of autologous fat graft resorption.

Methods:

The fatty cushion of the inguinal region of 20 female adult Wistar rats was removed and then autografted, using a standard volume of 0.2 ml in the subfascial plane of the dorsal region. The subject animals were randomized into two groups, the control and study groups. The study group animals were administered 20 mg/kg/day of tamoxifen citrate over a period of 21 days, by means of gavage. At the end of the experiment, the animals were killed and the grafts underwent morphologic and histopathologic analysis, with emphasis on the predominant inflammatory response pattern and collagen maturation.

Results:

The rats undergoing treatment with tamoxifen (study group) presented higher values in relation to the weight and volume of fat grafts compared with the initial values and the control group. Histologic analysis using hematoxylin and eosin staining showed that resolution of the inflammatory process was faster in the control group. Analysis using the picrosirius method demonstrated higher percentages of immature collagen versus mature collagen.

Conclusion:

Use of tamoxifen reduced the rates of resorption and fibrosis of the injected fat, resulting in better integration of the autologous fat graft.
Intralesional Laser Treatment for Dermal Filler Complications
Authors: Schelke Leonie W. , Decates Tom S. , van der Lugt Claudia I. M. , Pelzer Levi , de Mey Gabrielle , Velthuis Peter J.
Published: May 2018

Background:

For complications caused by filler treatments, in general, two treatment regimens are advised: systemic drugs and surgical removal of the material. Another possible treatment option would be removal of the material by intralesional laser treatment.

Methods:

Two hundred forty-two patients with complications caused by fillers were treated with intralesional laser treatment.

Results:

In the majority of patients, an improvement was achieved (92 percent), in 9 percent the complication was resolved, and in 3 percent it was not improved (unknown in the rest).

Conclusion:

Considering the large number of patients treated until now and the efficacy and good safety profile of this treatment, the authors plead that intralesional laser treatment may be considered as a treatment option before surgery.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Adipofascial Flaps With Acellular Dermal Matrix Compared With Myocutaneous Flap Reconstruction in Lumbar Myelomeningocele Defects
Authors: Pourtaheri Navid , Wang Derek , Calva Daniel , Chopra Karan , Kumar Anand R.
Published: May 2018

Background:

Adipofascial flaps (AFF) with acellular dermal matrix (ADM) have the potential to reconstruct neural tube defects without sacrificing muscle that may be critical for long-term function. Comparative studies between myocutaneous flap (MF) reconstruction, the accepted standard reconstructive technique, and AFF/ADM remain under-reported. The aim of this study was to evaluate the safety and efficacy of myelomeningocele reconstruction using muscle sparing AFF/ADM versus MF.

Methods:

A retrospective comparison was conducted on consecutive myelomeningocele patients reconstructed with MF or AFF/ADM over an 84-month period. Data analyzed included: basic demographics, defect size, reconstructive technique, complications, and length of follow-up. A supplemental meta-analysis based on systematic review of literature was performed to compare alternative reconstructive options.

Results:

Twelve patients were identified who met inclusion criteria. Median age, weight, and defect size at reconstruction in the AFF/ADM group (n = 6) was 37.5 weeks, 3.25 kg, and 20.0 cm2, respectively, and in the MF group (n = 6) was 37 weeks, 3.6 kg, and 22.5 cm2 (P > 0.5). For the AFF/ADM versus MF groups, median follow-up was 33.8 versus 22.6 months, reoperation rate was 0% versus 17% (P = 1.0), and complex skin flap closure rate was 17% versus 100% (P = 0.015). No cerebrospinal fluid leaks or surgical site infections occurred in either group. Meta-analysis of the literature revealed no statistically significant difference in complications rates between muscle and nonmuscle flap reconstruction (P > 0.5); potential long-term sequelae of muscle flap harvest were not included.

Conclusions:

Muscle sparing AFF with ADM is a safe and effective surgical alternative to muscle flaps for lumbar myelomeningocele reconstruction.
Face Transplant: Status of Current Supporting Technology to Plan and Perform the Operation and Monitor the Graft in the Postoperative Period
Authors: Caterson Edward J. , McCarty Justin C.
Published: May 2018

Face transplant has rapidly advanced since the first operation in 2005, and to date, 40 partial or full-face transplants have been performed. The safety and efficacy of this operation are aided at all phases by supporting technologies. These include advanced imaging techniques to plan the operation, devices to monitor the flap in the immediate perioperative period, and noninvasive imaging and serum markers to monitor for acute and chronic rejection. Some of the technologies, such as those used in the immediate perioperative period, have extensive evidence supporting their use, whereas those to detect acute or chronic rejection remain investigational. The technologies of today will continue to evolve and make the operation safer with improved outcomes; however, the most significant barrier for face transplant continues to be immunologic rejection.
The GalNAc-T Activation (GALA) Pathway: Drivers and Markers
Authors: Chia Joanne , Tay Felicia , Bard Frederic
Published: May 2018

The enzymes GALNTs add GalNAc sugar to Ser and Thr residues, forming the Tn glycan. GALNTs are activated by trafficking from Golgi to ER, a process driven by the Src kinase and negatively regulated by ERK8. This GALNTs activation (aka GALA) pathway induces high Tn levels and is a key driver of liver tumor growth. Recently, Tabak and colleagues have contested our previous data that EGF stimulation can induce GALNTs relocation. Here, we show that relocation induced by EGF is actually detectable in the images acquired by Tabak et al. Furthermore, we show that expression of EGFR enhances relocation and appears required to drive relocation induced by ERK8 depletion. We also propose that quantification of O-glycosylation of the ER resident protein PDIA4 provides an alternative measure of GALA. In sum, we demonstrate that non-reproducibility was due to experimental errors, that EGFR is indeed a driver of GALA and propose additional markers to facilitate the study of this pathway.
Streptococcal dTDP-L-rhamnose biosynthesis enzymes: functional characterization and lead compound identification
Authors: van der Beek Samantha L. , Zorzoli Azul , Çanak Ebru , Chapman Robert N. , Meyer Benjamin H. , Boons Geert-Jan , Dorfmueller Helge C. , van Sorge Nina M.
Published: May 2018

Biosynthesis of the nucleotide sugar precursor dTDP-L-rhamnose is critical for the viability and virulence of many human pathogenic bacteria, includingStreptococcus pyogenes(Group AStreptococcus; GAS) andStreptococcus mutans. Those pathogens require dTDP-L-rhamnose for the production of structurally similar rhamnose polysaccharides in their cell wall. Via heterologous expression inS. mutans, we confirm that GAS RmlB and RmlC are critical for dTDP-L-rhamnose biosynthesis through their action as dTDP-glucose-4,6-dehydratase and dTDP-4-keto-6-deoxyglucose-3,5-epimerase enzymes, respectively. Complementation with GAS RmlB and RmlC containing specific point mutations corroborated the conservation of previous identified catalytic residues in these enzymes. Bio-layer interferometry was used to identify and confirm inhibitory lead compounds that bind to GAS dTDP-rhamnose biosynthesis enzymes RmlB, RmlC and GacA. One of the identified compounds, Ri03, inhibited growth of GAS as well as several other rhamnose-dependent streptococcal pathogens with an MIC50of 120-410 μM. We therefore conclude that inhibition of dTDP-L-rhamnose biosynthesis such as Ri03 affect streptococcal viability and can serve as a lead compound for the development of a new class of antibiotics that targets dTDP-rhamnose biosynthesis in pathogenic bacteria.
IL-17RA-signaling modulates CD8+ T cell survival and exhaustion duringTrypanosoma cruziinfection
Authors: Boari Jimena Tosello , Furlan Cintia L. Araujo , Vernengo Facundo Fiocca , Rodriguez Constanza , Ramello María C. , Vesely María C. Amezcua , Serrán Melisa Gorosito , Nuñez Nicolás G. , Richer Wilfrid , Piaggio Eliane , Montes Carolina L. , Gruppi Adriana , Rodríguez Eva V. Acosta
Published: May 2018

The IL-17 family contributes to host defense against many intracellular pathogens by mechanisms not fully understood. CD8+ T lymphocytes are key elements against intracellular microbes and their survival and appropriate response is orchestrated by several cytokines. Here, we demonstrated that IL-17RA-signaling cytokines sustain pathogen-specific CD8+ T cell immunity. Absence of IL-17RA and IL-17A/F duringTrypanosoma cruziinfection resulted in increased tissue parasitism and reduced frequency of parasite-specific CD8+ T cells. Impaired IL-17RA-signalingin vivoincreased apoptosis of parasite-specific CD8+ T cells while recombinant IL-17in vitrodown-regulated the pro-apoptotic protein BAD and promoted activated CD8+ T cell survival. Phenotypic, functional and trancriptomic profiling showed thatT. cruzi-specific CD8+ T cells arising in IL-17RA-deficient mice presented features of cell dysfunction. PD-L1 blockade partially restored the magnitude of CD8+ T cell responses and parasite control in these mice. Adoptive transfer experiments established that IL-17RA-signaling is intrinsically required for the proper maintenance of functional effector CD8+ T cells. Altogether, our results identify IL-17RA and IL-17A as critical factors for sustaining CD8+ T cell immunity toT. cruzi.
Identification of cryptic stator subunits from an apicomplexan ATP synthase
Authors: Huet Diego , Rajendran Esther , Dooren Giel G. Van , Lourido Sebastian
Published: May 2018

The mitochondrial ATP synthase is a macromolecular motor that uses the proton gradient to generate ATP. Proper ATP synthase function requires a stator linking the catalytic and rotary portions of the complex. However, sequence-based searches fail to identify genes encoding stator subunits in apicomplexan parasites like Toxoplasma gondii or the related organisms that cause malaria. Here, we identify 11 previously unknown subunits from the Toxoplasma ATP synthase, which lack homologs outside the phylum. Hidden Markov modeling suggests that two of them—ICAP2 and ICAP18—share distant homology with mammalian stator subunits. Our analysis shows that both proteins form part of the ATP synthase complex. Depletion of ICAP2 leads to aberrant mitochondrial morphology, decreased oxygen consumption, and disassembly of the complex, consistent with its role as an essential component of the Toxoplasma ATP synthase. Our findings highlight divergent features of the central metabolic machinery in apicomplexans, which may reveal new therapeutic opportunities.
Regulation of the error-prone DNA polymerase polκ by oncogenic signaling and its contribution to drug resistance
Authors: Temprine Kelsey , Langdon Erin M , Mehta Krisha , Clapp Averill , White Richard M
Published: May 2018

Mutations in the proofreading domains of the replicative DNA polymerases polδ and polε are associated with elevated mutation rates in cancer, but the roles of other DNA polymerases in tumorigenesis remain poorly understood. One such polymerase is polκ, an enzyme that plays a key role in translesion synthesis. polκ contributes to cell survival in the face of DNA damage but can be highly mutagenic due to lack of a proofreading domain. Here we demonstrate that cancer cells under stress from oncogene inhibition upregulate polκ and shift its localization from the cytoplasm to the nucleus. This effect can be phenocopied by mTOR inhibition or glucose deprivation, analogous to stress-induced mutagenesis inE. coliwhereby cell stress and nutrient deprivation can upregulate and activate DinB/pol IV (the bacterial orthologue of polκ). We find that cancer cells normally sequester polκ in the cytoplasm via exportin-1, likely to prevent excess mutagenesis from the error-prone nature of this polymerase. Subverting the normal nuclear-cytoplasmic shuttling by forced overexpression of nuclear polκ increases resistance of melanoma cells to the BRAFV600Einhibitor vemurafenib. This data suggests a mechanism by which cancer cells regulate the expression and localization of the error-prone polymerase polκ, abrogation of which can contribute to drug resistance.

One Sentence Summary:Cancer cells under stress from oncogene or mTOR inhibition dysregulate the error-prone DNA polymerase polκ, which contributes to drug resistance in melanoma cells.
PathogenicDDX3Xmutations impair RNA metabolism and neurogenesis during fetal cortical development
Authors: Lennox Ashley L. , Jiang Ruiji , Suit Lindsey , Fregeau Brieana , Sheehan Charles J. , Aldinger Kimberly A. , Moey Ching , Lobach Iryna , Mirzaa Ghayda , Afenjar Alexandra , Babovic-Vuksanovic Dusica , Bézieau Stéphane , Blackburn Patrick R. , Bunt Jens , Burglen Lydie , Charles Perrine , Chung Brian H.Y. , Cogné Benjamin , DeBrosse Suzanne , Di Donato Nataliya , Faivre Laurence , Héron Delphine , Innes A. Micheil , Isidor Bertrand , Johnson-Kerner Bethany L. , Keren Boris , Kimball Amy , Klee Eric W. , Kuentz Paul , Küry Sébastien , Martin-Coignard Dominique , Mignot Cyril , Miyake Noriko , Nava Caroline , Nizon Mathilde , Rodriguez Diana , Blok Lot Snijders , Thauvin-Robinet Christel , Thevenon Julien , Vincent Marie , Ziegler Alban , Dobyns William , Richards Linda J. , Barkovich A. James , Floor Stephen N. , Silver Debra L. , Sherr Elliott H.
Published: May 2018

De novogermline mutations in the RNA helicaseDDX3Xaccount for 1-3% of unexplained intellectual disability (ID) cases in females, and are associated with autism, brain malformations, and epilepsy. Yet, the developmental and molecular mechanisms by whichDDX3Xmutations impair brain function are unknown. Here we use human and mouse genetics, and cell biological and biochemical approaches to elucidate mechanisms by which pathogenicDDX3Xvariants disrupt brain development. We report the largest clinical cohort to date withDDX3Xmutations (n=78), demonstrating a striking correlation between recurrent dominant missense mutations, polymicrogyria, and the most severe clinical outcomes. We show thatDdx3xcontrols cortical development by regulating neuronal generation and migration. SevereDDX3Xmissense mutations profoundly disrupt RNA helicase activity and induce ectopic RNA-protein granules and aberrant translation in neural progenitors and neurons. Together, our study demonstrates novel mechanisms underlyingDDX3Xsyndrome, and highlights roles for RNA-protein aggregates in the pathogenesis of neurodevelopmental disease.
Microbial Reduction of Metal-Organic Frameworks Enables Synergistic Chromium Removal
Authors: Springthorpe Sarah K. , Dundas Christopher M. , Keitz Benjamin K.
Published: May 2018

Microbe-material redox interactions underpin many emerging technologies, including bioelectrochemical cells and bioremediation. However, commonly utilized material substrates, such as metal oxides, suffer from a lack of tunability and can be challenging to characterize. In contrast, metal-organic frameworks, a class of porous materials, exhibit well-defined structures, high crystallinity, large surface areas, and extensive chemical tunability. Here, we report that metal-organic frameworks can support the growth of the electroactive bacterium Shewanella oneidensis. Specifically, we demonstrate that Fe(III)-containing frameworks, MIL-100 and Fe-BTC, can be reduced by the bacterium via its extracellular electron transfer pathways and that reduction rate/extent is tied to framework structure, surface area, and particle morphology. In a practical application, we show that cultures containing S. oneidensis and reduced frameworks can remediate lethal concentrations of Cr(VI), and that pollutant removal exceeds the performance of either component in isolation or bioreduced iron oxides. Repeated cycles of Cr(VI) dosing had little effect on bacterial viability or Cr(VI) adsorption capacity, demonstrating that the framework confers protection to the bacteria and that no regenerative step is needed for continued bioremediation. In sum, our results show that metal-organic frameworks can serve as microbial respiratory substrates and suggest that they may offer a promising alternative to metal oxides in applications seeking to combine the advantages of bacterial metabolism and synthetic materials.
PRX9andPRX40are extensin peroxidases essential for maintaining tapetum and microspore cell wall integrity duringArabidopsisanther development
Authors: Jacobowitz Joseph R. , Weng Jing-Ke
Published: May 2018

Pollen and microspore development is an essential step in the life cycle of all land plants that generate male gametes. Within flowering plants, pollen development occurs inside of the anther. Here, we report the identification of two class III peroxidase-encoding genes,PRX9andPRX40, that are genetically redundant and essential for proper anther and pollen development inArabidopsis thaliana.Arabidopsisdouble mutants devoid of functionalPRX9andPRX40are male-sterile. The mutant anthers display swollen, hypertrophic tapetal cells and pollen grains, suggesting disrupted cell wall integrity. These phenotypes ultimately lead to nearly 100%-penetrant pollen degeneration upon anther maturation. Using immunochemical and biochemical approaches, we show thatPRX9andPRX40are likely extensin peroxidases that contribute to the establishment of tapetal cell wall integrity during anther development. This work identifiesPRX9andPRX40as the first extensin peroxidases to be described inArabidopsisand highlights the importance of extensin cross-linking during plant development.
Global transcriptional analysis ofGeobacter sulfurreducensunder palladium reducing conditions reveals new key cytochromes involved
Authors: Hernández-Eligio Alberto , Pat-Espadas Aurora M. , Vega-Alvarado Leticia , Huerta-Amparán Manuel , Cervantes Francisco J. , Juárez Katy
Published: May 2018

Geobacter sulfurreducensis capable of reducing Pd(II) to Pd(0) using acetate as electron donor; however, the biochemical and genetic mechanisms involved in this process have not been described. In this work, we carried out transcriptome profiling analysis to identify the genes involved in Pd(II) reduction in this bacterium. Our results showed that 252 genes were upregulated while 141 were downregulated during Pd(II) reduction. Among the upregulated genes, 12 were related to energy metabolism and electron transport; 50 were classified as involved in protein synthesis; 42 were associated with regulatory functions and transcription, and 47 have no homologs with known function. RT-qPCR data confirmed upregulation of genes encoding PilA, the structural protein for the electrically conductive pili, as well asc-type cytochromes GSU1062, GSU2513, GSU2808, GSU2934, GSU3107, OmcH, OmcM, PpcA, PpcD under Pd(II)-reducing conditions. ΔpilAand ΔpilRmutant strains showed 20% and 40% decrease in the Pd(II)-reducing capacity, respectively, compared to the wild type strain, indicating the central role of the pili in this process. RT-qPCR data collected during Pd(II) reduction also confirmed downregulation of theomcB, omcC, omcZ,andomcSgenes, which have been shown to be involved in Fe(III) reduction and electrodes. Based on these results, we propose mechanisms involved in Pd(II) reduction byG. sulfurreducens.

Importance

Geobacter sulfurreducensis a versatile microorganism, known for its ability to reduce a wide range of environmentally relevant metals. It has been reported that this bacterium synthesizes palladium nanoparticles successfully. Yet, the biochemical and genetic mechanisms involved in this process had not been described previously. By using a transcriptome profile analysis to identify genes implicated in this process and genetic and physiological data, we propose a model for the biological reduction of Pd(II) byG. sulfurreducens. Moreover, the study also revealed the microbial reduction of Pd(II) coupled to growth, which shows not only unexpected ideas about its complex metabolism, but some key cytochromes involved in this pathway, which have not been previously associated with other metal reducing process for this bacterium. In brief the present work contributes to a better understanding of the biochemical and genetic mechanisms involved in Pd(II) reduction and put forward novel insights aboutG. sulfurreducensmetabolism.
Recalibration of path integration in hippocampal place cells
Authors: Jayakumar Ravikrishnan P. , Madhav Manu S. , Savelli Francesco , Blair Hugh T. , Cowan Noah J. , Knierim James J.
Published: May 2018

Hippocampal place cells are spatially tuned neurons that serve as elements of a “cognitive map” in the mammalian brain1. To detect the animal’s location, place cells are thought to rely upon two interacting mechanisms: sensing the animal’s position relative to familiar landmarks2,3and measuring the distance and direction that the animal has travelled from previously occupied locations4–7. The latter mechanism, known aspath integration, requires a finely tuned gain factor that relates the animal’s self-movement to the updating of position on the internal cognitive map, with external landmarks necessary to correct positional error that eventually accumulates8,9. Path-integration-based models of hippocampal place cells and entorhinal grid cells treat the path integration gain as a constant9–14, but behavioral evidence in humans suggests that the gain is modifiable15. Here we show physiological evidence from hippocampal place cells that the path integration gain is indeed a highly plastic variable that can be altered by persistent conflict between self-motion cues and feedback from external landmarks. In a novel, augmented reality system, visual landmarks were moved in proportion to the animal’s movement on a circular track, creating continuous conflict with path integration. Sustained exposure to this cue conflict resulted in predictable and prolonged recalibration of the path integration gain, as estimated from the place cells after the landmarks were extinguished. We propose that this rapid plasticity keeps the positional update in register with the animal’s movement in the external world over behavioral timescales (mean 50 laps over 35 minutes). These results also demonstrate that visual landmarks not only provide a signal to correct cumulative error in the path integration system, as has been previously shown4,8,16–19, but also rapidly fine-tune the integration computation itself.
Recruitment of occipital cortex by arithmetic processing follows computational bias in early blind
Authors: Crollen Virginie , Lazzouni Latifa , Bellemare Antoine , Rezk Mohamed , Lepore Franco , Noël Marie-Pascale , Seron Xavier , Collignon Olivier
Published: May 2018

Arithmetic reasoning activates the occipital cortex of early blind people (EB). This activation of visual areas may reflect functional flexibility or the intrinsic computational role of specific occipital regions. We contrasted these competing hypotheses by characterizing the brain activity of EB and sighted participants while performing subtraction, multiplication and a control verbal task. In both groups, subtraction selectively activated a bilateral dorsal network commonly activated during spatial processing. Multiplication triggered more activity in temporal regions thought to participate in memory retrieval. No between-group difference was observed for the multiplication task whereas subtraction induced enhanced activity in the right dorsal occipital cortex of the blind individuals only. As this area overlaps and exhibits increased functional connectivity with regions showing selective tuning to auditory spatial processing, our results suggest that the recruitment of occipital regions during high-level cognition in the blind actually relates to the intrinsic computational role of the reorganized regions.
Glycosylation-associated dysregulation of pyocyanin production inPseudomonas aeruginosa: Implications for quorum sensing regulation
Authors: McClinton Anna K. , Hamilton Caleb L. , Cioffi Donna L. , Cioffi Eugene A.
Published: May 2018

Pseudomonas aeruginosa(P. aeruginosa) is an important opportunistic pathogen associated with high mortality in pneumonia, sepsis, and cystic fibrosis. Lending to its ability to cause severe disease and death is its arsenal of virulence factors and host evasion tactics. In addition to various other regulatory systems, many ofP. aeruginosa’s virulence factors are regulated by a population density dependent regulatory network known as quorum sensing (QS). Many regulatory systems are impacted by post-translational modifications of proteins. An underexplored physiological aspect ofP. aeruginosais its ability to glycosylate proteins and the subsequent impact of glycosylation onP. aeruginosaphysiology and behavior. The goal of this study was to determine whetherP. aeruginosaQS is regulated by glycosylation. Here we demonstrate that disruption of glycosylation dysregulates QS phenotypes, notably pyocyanin production, inP. aeruginosaPAO1. In this study, it was initially observed that deletion of theP. aeruginosaneuraminidase, PaNA, caused an increased production of pyocyanin in LB-Lennox broth compared to wildtype bacteria at identical population densities. To confirm that the increased pyocyanin production was due to QS, we performed induction experiments using 10% cell-free media harvested from overnight cultures. To determine whether the QS phenotype observed is specific to pseudaminic acid, the target of PaNA, or if it is a reflection of global changes in glycosylation, we measured QS in a library of mutant bacteria generated in an MPAO1 background containing transposon insertions in various glycosyl-associated enzymes. The pattern of dysregulated QS held true in these mutant strains as well. Overall these data indicate that inP. aeruginosa, glycosylation is an important determinant of QS.
Mouse models of hereditary hemochromatosis do not develop early liver fibrosis in response to a high fat diet
Authors: Wagner John , Fillebeen Carine , Haliotis Tina , Mui Jeannie , Vali Hojatollah , Pantopoulos Kostas
Published: May 2018

Hepatic iron overload, a hallmark of hereditary hemochromatosis (HH), triggers progressive liver disease. There is also increasing evidence for a pathogenic role of iron in non-alcoholic fatty liver disease (NAFLD), which may progress to non-alcoholic steatohepatitis (NASH), fibrosis, cirrhosis and hepatocellular cancer. Mouse models of HH and NAFLD can be used to explore potential interactions between iron and lipid metabolic pathways. Hfe−/− mice, a model of moderate iron overload, were reported to develop early liver fibrosis in response to a high fat diet. However, this was not the case with Hjv−/− mice, a model of severe iron overload. These data raised the possibility that the Hfe gene may protect against liver injury independently of its iron regulatory function. Herein, we addressed this hypothesis in a comparative study utilizing wild type, Hfe−/−, Hjv−/− and double Hfe−/−Hjv−/− mice. The animals, all in C57/BL6 background, were fed with a high fat diet for 14 weeks and developed hepatic steatosis, associated with mild iron overload. Hfe co-ablation did not sensitize steatotic Hjv-deficient mice to liver injury. Moreover, we did not observe any signs of liver inflammation or fibrosis even in single steatotic Hfe−/− mice. Ultrastructural studies revealed a reduced lipid and glycogen content in Hjv−/− hepatocytes, indicative of a metabolic defect. Interestingly, glycogen levels were restored in double Hfe−/−Hjv−/− mice, which is consistent with a metabolic function of Hfe. We conclude that hepatocellular iron excess does not aggravate diet-induced steatosis to steatohepatitis or early liver fibrosis in mouse models of HH, irrespectively of the presence or lack of Hfe.
Clustering of Type 2 Diabetes Genetic Loci by Multi-Trait Associations Identifies Disease Mechanisms and Subtypes
Authors: Udler Miriam S. , Kim Jaegil , von Grotthuss Marcin , Bonàs-Guarch Sílvia , Mercader Josep M , Cole Joanne B. , Chiou Joshua , Anderson Christopher D , Boehnke Michael , Laakso Markku , Atzmon Gil , Glaser Benjamin , Gaulton Kyle , Flannick Jason , Getz Gad , Florez Jose C.
Published: May 2018

Background

Type 2 diabetes (T2D) is a heterogeneous disease for which 1) disease-causing pathways are incompletely understood and 2) sub-classification may improve patient management. Unlike other biomarkers, germline genetic markers do not change with disease progression or treatment. In this paper we test whether a germline genetic approach informed by physiology can be used to deconstruct T2D heterogeneity. First, we aimed to categorize genetic loci into groups representing likely disease mechanistic pathways. Second, we asked whether the novel clusters of genetic loci we identified have any broad clinical consequence, as assessed in four independent cohorts of individuals with T2D.

Methods and Findings

In an effort to identify mechanistic pathways driven by established T2D genetic loci, we applied Bayesian nonnegative matrix factorization clustering to genome-wide association results for 94 independent T2D genetic loci and 47 diabetes-related traits. We identified five robust clusters of T2D loci and traits, each with distinct tissue-specific enhancer enrichment based on analysis of epigenomic data from 28 cell types. Two clusters contained variant-trait associations indicative of reduced beta-cell function, differing from each other by high vs. low proinsulin levels. The three other clusters displayed features of insulin resistance: obesity-mediated (high BMI, waist circumference), “lipodystrophy-like” fat distribution (low BMI, adiponectin, HDL-cholesterol, and high triglycerides), and disrupted liver lipid metabolism (low triglycerides). Increased cluster GRS’s were associated with distinct clinical outcomes, including increased blood pressure, coronary artery disease, and stroke risk. We evaluated the potential for clinical impact of these clusters in four studies containing participants with T2D (METSIM, N=487; Ashkenazi, N=509; Partners Biobank, N=2,065; UK Biobank N=14,813). Individuals with T2D in the top genetic risk score decile for each cluster reproducibly exhibited the predicted cluster-associated phenotypes, with ~30% of all participants assigned to just one cluster top decile.

Conclusion

Our approach identifies salient T2D genetically anchored and physiologically informed pathways, and supports use of genetics to deconstruct T2D heterogeneity. Classification of patients by these genetic pathways may offer a step toward genetically informed T2D patient management.
Cell type-dependent effects of ellagic acid on cellular metabolism
Authors: Boehning Alexandra L. , Essien Safia A. , Underwood Erica L. , Dash Pramod K. , Boehning Darren
Published: May 2018

Ellagic acid is a botanical polyphenol which has been shown to have numerous effects on cellular function. Ellagic acid can induce apoptosis and inhibit the proliferation of various cancer cell types in vitro and in vivo. As such, ellagic acid has attracted significant interest as a potential chemotherapeutic compound. One mechanism by which ellagic acid has been proposed to affect cellular physiology is by regulating metabolic pathways. Here we show the dose-dependent effects of ellagic acid on cellular energy production and downstream induction of the apoptotic program in HEK293, HeLa, MCF7, and HepG2 cells. At physiologically relevant doses, eallgic acid has pleiotropic and cell-type specific effects on mitochondrial function. At high doses ellagic acid can also influence glycolytic pathways and induce cell death. Our results demonstrate that ellagic acid can influence mitochondrial function at therapeutically relevant concentrations. The observed effects of ellagic acid on cellular respiration are complex and cell type-specific, which may limit the chemotherapeutic utility of this compound.
Global biogeographical regions of freshwater fish species
Authors: Leroy Boris , Dias Murilo S. , Giraud Emilien , Hugueny Bernard , Jézéquel Céline , Leprieur Fabien , Oberdorff Thierry , Tedesco Pablo A.
Published: May 2018

Aim

To define the major biogeographical regions and transition zones for freshwater fish species.

Taxon

Strictly freshwater species of actinopterygian fish (i.e., excluding marine and amphidromous fish families).

Methods

We based our bioregionalisation on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11 295 species in 2 581 basins. On the basis of this dataset, we generated a bipartite (basin-species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions.

Results

Our bioregionalisation scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino-Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic).

Main conclusions

Our results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater-specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations, and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10 to 20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions.
Aurora B is required for programmed variations of cytokinesis during morphogenesis in theC. elegansembryo
Authors: Bai Xiaofei , Lee Po-Yi , Chen Chin-Yi , Simmons James R. , Nebenfuehr Benjamin , Mitchell Diana , Klebanow Lindsey R. , Mattson Nicholas , Sorensen Turpin Christopher G. , Chen Bi-Chang , Betzig Eric , Bembenek Joshua N.
Published: May 2018

While cytokinesis has been intensely studied, how it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariantC. elegansembryo lineage and found several reproducibly altered parameters at different stages. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we find several unexpected alterations including migration of midbodies to the apical surface during epithelial polarization in different tissues. Aurora B kinase, which is essential for several aspects of cytokinesis, remains localized to the apical membrane after internalization of other midbody components. Inactivation of Aurora B causes cytokinesis failure, which disrupts polarization and tissue formation. Therefore, cytokinesis shows surprising diversity during development and is required during epithelial polarization to establish cellular architecture during morphogenesis.
Whole-genome deep learning analysis reveals causal role of noncoding mutations in autism
Authors: Zhou Jian , Park Christopher Y. , Theesfeld Chandra L. , Yuan Yuan , Sawicka Kirsty , Darnell Jennifer C. , Scheckel Claudia , Fak John J , Tajima Yoko , Darnell Robert B. , Troyanskaya Olga G.
Published: May 2018

We address the challenge of detecting the contribution of noncoding mutations to disease with a deep-learning-based framework that predicts specific regulatory effects and deleterious disease impact of genetic variants. Applying this framework to 1,790 Autism Spectrum Disorder (ASD) simplex families reveals autism disease causality of noncoding mutations by demonstrating that ASD probands harbor transcriptional (TRDs) and post-transcriptional (RRDs) regulation-disrupting mutations of significantly higher functional impact than unaffected siblings. Importantly, we detect this significant noncoding contribution at each level, transcriptional and post-transcriptional, independently and after multiple hypothesis correction. Further analysis suggests involvement of noncoding mutations in synaptic transmission and neuronal development, and reveals a convergent genetic landscape of coding and noncoding (TRD and RRD) de novo mutations in ASD. We demonstrate that sequences carrying prioritized proband de novo mutations possess transcriptional regulatory activity and drive expression differentially, and highlight a link between noncoding mutations and IQ heterogeneity in ASD probands. Our predictive genomics framework illuminates the role of noncoding mutations in ASD, prioritizes high impact transcriptional and post-transcriptional regulatory mutations for further study, and is broadly applicable to complex human diseases.
Functional instability allows access to DNA in longer Transcription Activator-Like Effector (TALE) arrays
Authors: Geiger-Schuller Kathryn , Mitra Jaba , Ha Taekjip , Barrick Doug
Published: May 2018

Transcription activator-like effectors (TALEs) bind DNA through an array of tandem 34-residue repeats. Here, we examine the kinetics of DNA binding for a set of TALE arrays with varying numbers of identical repeats using single molecule microscopy. Using a new deterministic modeling approach, we find evidence for conformational heterogeneity in both the free- and DNA-bound TALE arrays. Combined with previous work demonstrating populations of partly folded TALE states, our findings reveal a functional instability in TALE-DNA binding. For TALEs forming less than one superhelical turn around DNA, partly folded open states inhibit DNA binding. In contrast, for TALEs forming more than one turn, the partly folded open states facilitate DNA binding. Overall, we find that increasing repeat number results in significantly slower interconversion between the various DNA-free and DNA-bound states. These findings highlight the role of conformational heterogeneity and dynamics in facilitating macromolecular complex assembly.

Impact Statement

Single molecule DNA-binding trajectories and deterministic modeling analyses demonstrate a functional role for high energy partly folded states in Transcription Activator-Like Effectors (TALEs) that could improve future TALEN design.
Genetic effects on promoter usage are highly context-specific and contribute to complex traits
Authors: Alasoo Kaur , Rodrigues Julia , Danesh John , Freitag Daniel F. , Paul Dirk S. , Gaffney Daniel J.
Published: May 2018

Genetic variants regulating RNA splicing and transcript usage have been implicated in both common and rare diseases. Although transcript usage quantitative trait loci (tuQTLs) have now been mapped in multiple cell types and conditions, the molecular mechanisms through which these variants exert their effect have remained elusive. Specifically, changes in transcript usage could arise from promoter choice, alternative splicing or 3′ end choice, but current tuQTL studies have not been able to distinguish between them. Here, we performed comprehensive analysis of RNA-seq data from human macrophages exposed to a range of inflammatory stimuli (IFNγ, Salmonella, IFNγ + Salmonella) and a metabolic stimulus (acetylated LDL), obtained from up to 84 individuals. In addition to conventional gene-level and transcript-level analyses, we also developed an analytical approach to directly quantify promoter, internal exon and 3′ end usage. We found that although naive transcript-level analysis often links single genetic variants to multiple coupled changes on the transcriptome, this appears to be an artefact of incomplete transcript annotations. Most of this coupling disappears when promoters, splicing and 3′ end usage are quantified directly. Furthermore, promoter, splicing and 3′ end QTLs are each enriched in distinct genomic features, suggesting that they are predominantly controlled by independent regulatory mechanisms. We also find that promoter usage QTLs are 50% more likely to be context-specific than canonical splicing QTLs and constitute 25% of the transcript-level colocalisations with complex traits. Thus, promoter usage might be a previously underappreciated molecular mechanism mediating complex trait associations in a context-specific manner.
Synchronization dependent on spatial structures of a mesoscopic whole-brain network
Authors: Choi Hannah , Mihalas Stefan
Published: May 2018

We study how the spatial structure of connectivity shapes synchronization in a system of coupled phase oscillators on a mammalian whole-brain network at the mesoscopic level. Complex structural connectivity of the mammalian brain is believed to underlie the versatility of neural computations. The Allen Mouse Brain Connectivity Atlas constructed from viral tracing experiments together with a new mapping algorithm reveals that the connectivity has a significant spatial dependence: the connection strength decreases with distance between the regions, following a power law. However, there are a number of residuals above the power-law fit, predominantly for long-range connections. We show how these strong connections between distal brain regions promote rapid transitions between highly localized synchronization and more global synchronization as the amount of dispersion in the frequency distribution changes. This may explain the brain’s ability to switch rapidly between global and modularized computations.
Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis
Authors: Mayrhofer Markus , De Laere Bram , Whitington Tom , Van Oyen Peter , Ghysel Christophe , Ampe Jozef , Ost Piet , Demey Wim , Hoekx Lucien , Schrijvers Dirk , Brouwers Barbara , Lybaert Willem , Everaert Els , De Maeseneer Daan , Strijbos Michiel , Bols Alain , Fransis Karen , Oeyen Steffi , van Dam Pieter-Jan , Van den Eynden Gert , Rutten Annemie , Aly Markus , Nordström Tobias , Van Laere Steven , Rantalainen Mattias , Rajan Prabhakar , Egevad Lars , Ullén Anders , Yachnin Jeffrey , Dirix Luc , Grönberg Henrik , Lindberg Johan
Published: May 2018

Background

There are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potential to cost-efficiently accelerate precision medicine trials to improve clinical efficacy and diminish costs and toxicity. However, comprehensive ctDNA profiling in metastatic prostate cancer to date has been limited.

Methods

A combination of targeted- and low-pass whole genome sequencing was performed on plasma cell-free DNA and matched white blood cell germline DNA in 364 blood samples from 217 metastatic prostate cancer patients.

Results

ctDNA was detected in 85.9% of baseline samples, correlated to line of therapy and was mirrored by circulating tumor cell enumeration of synchronous blood samples. Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-ARstructural variation, from 15.4% during first line mCRPC therapy to 45.2% in fourth line, indicating a continuous evolution of AR during the course of the disease. Patients displayed frequent alterations in DNA repair deficiency genes (18.0%). Additionally, the microsatellite instability phenotype was identified in 3.81% of eligible samples (≥0.1 ctDNA fraction). Sequencing of non-repetitive intronic- and exonic regions ofPTEN, RB1andTP53detected biallelic inactivation in 47.5%, 20.3% and 44.1% of samples with ≥0.2 ctDNA fraction, respectively. Only one patient carried a clonal high-impact variant without a detectable second hit. Intronic high-impact structural variation was twice as common as exonic mutations inPTENand RB1. Finally, 14.6% of patients presented false positive variants due to clonal hematopoiesis, commonly ignored in commercially available assays.

Conclusions

ctDNA profiles appear to mirror the genomic landscape of metastatic prostate cancer tissue and may cost-efficiently provide somatic information in clinical trials designed to identify predictive biomarkers. However, intronic sequencing of the interrogated tumor suppressors challenge the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous assignments which in turn may confound results and impede true associations in clinical trials.