bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of Hoxc genes in the development of the limb integumentary organ (nail, claw, or hoof)
Authors: Lasierra Maria Angeles Ros , Fernández‐Guerrero Marc , Delisle Lucille , Yakushiji‐Kaminatsui Nayuta , Darbellay Fabrice , Pérez‐Gómez Rocío , Duboule Denis
Published: April 2018

The developing vertebrate limb has long proved as an excellent system for studying the mechanisms involved in pattern formation and morphogenesis and more recently in transcriptional regulation and morphological evolution. To elucidate the stage‐specific expression profiles of the components of the developing limb, we have generated the temporal transcriptome of the limb progenitors and of the overlying ectoderm separately. Our study has uncovered a collinear activation of Hoxc genes in the limb ectoderm that we have validated by in situ hybridization. However, while members of the HoxA and HoxD clusters show complex and dynamic patterns of expression during limb development that correlate with the morphology of the different limb segments, no specific function for the HoxC or HoxB clusters has been identified (1–3).

To investigate the function of Hoxc genes in the limb ectoderm, we have reexamined the HoxC cluster null mice. Remarkably, and despite exhibiting normal terminal phalanges, these mice didn't form claws (anonychia). Morphological and immunohistochemical analysis identified a failure in the differentiation of the main components of the nail/claw organ. To unravel the transcriptional regulation of Hoxc genes in the limb ectoderm, we used the ATACseq technique. Using this approach, we identified two putative regulatory regions which activity was tested in mouse transgenic enhancer assays.

It is currently considered that Hox genes have played a key role in the evolution of morphological traits, probably associated with changes in their regulatory landscapes (4). Given that the form and size of the distal limb integumentary organ (nail, claw or hoof) correlates with that of the distal phalanx and that the development of hooves was a major innovation in the evolution of a cursorial lifestyle, we are also exploring the possible implication of Hoxc genes in the nail/claw/hoof transition.

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Macrophage Polarization Favors Epithelial Repair During Acute Respiratory Distress Syndrome*
Authors: Garnier Marc , Gibelin Aude , Mailleux Arnaud A. , Leçon Véronique , Hurtado-Nedelec Margarita , Laschet Jamila , Trebbia Grégoire , Neuville Mathilde , Tanaka Sébastien , Crestani Bruno , Dehoux Monique , Quesnel Christophe
Published: April 2018

Objectives:

Alveolar macrophage polarization and role on alveolar repair during human acute respiratory distress syndrome remain unclear. This study aimed to determine during human acute respiratory distress syndrome: the alveolar macrophage polarization, the effect of alveolar environment on macrophage polarization, and the role of polarized macrophages on epithelial repair.

Design:

Experimental ex vivo and in vitro investigations.

Setting:

Four ICUs in three teaching hospitals.

Patients:

Thirty-three patients with early moderate-to-severe acute respiratory distress syndrome were enrolled for assessment of the polarization of alveolar macrophages.

Interventions:

Polarization of acute respiratory distress syndrome macrophages was studied by flow cytometry and quantitative polymerase chain reaction. Modulation of macrophage polarization was studied in vitro using phenotypic and functional readouts. Macrophage effect on repair was studied using alveolar epithelial cells in wound healing models.

Measurements and Main Results:

Ex vivo, alveolar macrophages from early acute respiratory distress syndrome patients exhibited anti-inflammatory characteristics with high CD163 expression and interleukin-10 production. Accordingly, early acute respiratory distress syndrome-bronchoalveolar lavage fluid drives an acute respiratory distress syndrome–specific anti-inflammatory macrophage polarization in vitro, close to that induced by recombinant interleukin-10. Culture supernatants from macrophages polarized in vitro with acute respiratory distress syndrome-bronchoalveolar lavage fluid or interleukin-10 and ex vivo acute respiratory distress syndrome alveolar macrophages specifically promoted lung epithelial repair. Inhibition of the hepatocyte growth factor pathway in epithelial cells and hepatocyte growth factor production in macrophages both reversed this effect. Finally, hepatocyte growth factor and soluble form of CD163 concentrations expressed relatively to macrophage count were higher in bronchoalveolar lavage fluid from acute respiratory distress syndrome survivors.

Conclusions:

Early acute respiratory distress syndrome alveolar environment drives an anti-inflammatory macrophage polarization favoring epithelial repair through activation of the hepatocyte growth factor pathway. These results suggest that macrophage polarization may be an important step for epithelial repair and acute respiratory distress syndrome recovery.
Treatment of Ingrowing Toenails With Phenol 88% or Trichloroacetic Acid 100%: A Comparative, Prospective, Randomized, Double-Blind Study
Authors: André Marie-Sophie , Caucanas Marie , André Josette , Richert Bertrand
Published: April 2018

BACKGROUND

Phenol is the gold standard for chemical matricectomy in ingrowing toenail. Recently, trichloroacetic acid (TCA) was used as cauterant. Both agents have high success rates but a postoperative healing time claimed to be faster for TCA rather than phenol.

OBJECTIVE

Comparing the efficacy, the postoperative oozing time, the inflammatory reaction, and the postoperative pain.

MATERIALS AND METHODS

Comparative, prospective, randomized, double-blind study. Eighty-four patients with 96 ingrowing toenails were randomized in 2 groups. Forty-six ingrowing toenails were treated with phenol 88% and 50 with TCA 100% within a 4-month period. Patients were observed 4 times for the presence of oozing and for the degree of inflammation. Patients assessed also oozing and pain on a scale basis during 34 days.

RESULTS

Oozing was observed to be less with phenol treatment, as from the second week. Inflammation was also significantly inferior in the phenol group at Week 4. Patients evaluated the incidence of pain below 2/10 for both cauterants, while oozing was higher with TCA during 34 days. The overall success rates of both groups were similar with 100%.

CONCLUSION

Phenol and TCA are both effective but TCA does not offer any advantage in terms of postoperative morbidity compared with phenol.
Influence of Disease Severity and Exercise Limitation on Exercise Training Intensity and Load and Health Benefits From Pulmonary Rehabilitation in Patients With COPD
Authors: Huynh Virginia C. , Fuhr Desi P. , Byers Bradley W. , Selzler Anne-Marie , Moore Linn E. , Stickland Michael K.
Published: April 2018

Purpose:

Some patients with chronic obstructive pulmonary disease (COPD) fail to achieve health benefits with pulmonary rehabilitation (PR). Exercise intensity and load represent stimulus for adaptation but it is unclear whether inappropriate exercise intensity and/or load are affected by severity of COPD, which may affect health benefits. The purpose was to determine whether COPD severity and/or the severity of pulmonary limitation to exercise (PLE) impacted exercising intensity or load and whether resultant intensity/load affected health outcomes derived from PR.

Methods:

Patients with COPD (n = 58, age = 67 ± 7 y, forced expiratory volume in the first second of expiration [FEV1] % predicted = 52 ± 21%) were recruited upon referral to PR. Primary health outcomes evaluated were 6-min walk distance and St George's Respiratory Questionnaire. Patients were stratified for disease severity using Global Initiative for Obstructive Lung Disease (GOLD) staging and PLE severity by change in inspiratory capacity during exercise. Exercise intensity and load were calculated from daily exercise records.

Results:

Participants achieved comparable training duration and load regardless of GOLD severity. Patients with more severe PLE achieved greater training duration (more severe: 546 ± 143 min., less severe: 451 ± 109 min., P = .036), and relative training load (more severe: 2200.8 ± 595.3 kcal, less severe: 1648.3 ± 597.8 kcal, P = .007). Greater overall training load was associated with greater improvements in 6-min walk distance (r = 0.24, P = .035). No significant relationships were observed between PLE, GOLD severity, training parameters, and St George's Respiratory Questionnaire response.

Conclusions:

Improvements in exercise tolerance can be explained by achieving greater training loads, demonstrating the importance of appropriate training load to maximize health outcomes in PR.
Is Inspiratory Muscle Weakness a Determinant of Endurance Exercise Tolerance During NIV-Supported Exercise in Patients With COPD?
Authors: Koch Rodrigo , Rapello Gabriel Victor Guimarães , de Tarso Müller Paulo
Published: April 2018

Purpose:

Previous research has reported that inspiratory muscle weakness is critical to decreased exercise tolerance and exercise tolerance improves with 10 cmH2O pressure support ventilation in patients with chronic obstructive pulmonary disease (COPD). The purpose of this study was to evaluate the effects of proportional assist ventilation (PAV) and continuous positive airway pressure (CPAP) compared with sham on exercise tolerance in patients with and without inspiratory muscle weakness.

Methods:

In a prospective design, 12 of 54 patients were eligible after clinical and comprehensive lung function evaluation, including maximum inspiratory pressure (MIP) measurement. Using baseline measures, participants were divided into 2 age-matched groups that differed in regard to MIP (Group 1, MIP <60 cmH2O, and Group 2, MIP ≥60 cmH2O). Each participant performed 3 constant work rate tests with noninvasive support (PAV, CPAP, sham) in random order on different days at 80% of maximal incremental power.

Results:

During the endurance tests, heart rate, peripheral oxygen saturation (Spo
2), dyspnea perception scale, and exercise tolerance were measured. There were no significant differences between groups for heart rate, Spo
2, dyspnea perception, or exercise tolerance during PAV, CPAP, or sham-supported exercise (P > .05 for all).

Conclusions:

In this small representative group of patients with COPD, inspiratory muscle weakness was not a determining factor of performance during CPAP or PAV-supported aerobic exercise.
Validation of the 5-Item Medication Adherence Report Scale in Older Stroke Patients in Iran
Authors: Lin Chung-Ying , Ou Huang-tz , Nikoobakht Mehdi , Broström Anders , Årestedt Kristofer , Pakpour Amir H.
Published: April 2018

Background:

There is a lack of feasible and validated measures to self-assess medication adherence for older patients with stroke. In addition, the potential determinants of medication adherence for older patients with stroke remain unclear.

Objectives:

The aims of this study were to (1) examine the psychometric properties of a 5-item questionnaire on medication adherence, specifically the 5-item Medication Adherence Report Scale (MARS-5), and (2) explore the determinants of medication adherence.

Methods:

Stroke patients older than 65 years (N = 523) filled out the MARS-5 and the Hospital Anxiety and Depression Scale. The medication possession rate (MPR) was calculated to measure the objective medication adherence. Several clinical characteristics (stroke types, blood pressure, comorbidity, HbA1c, quantity of prescribed drugs, fasting blood glucose, and total cholesterol) and background information were collected. We used Rasch analysis with a differential item functioning test to examine psychometric properties.

Results:

All 5 items in the MARS-5 fit in the same construct (ie, medication adherence), no differential item functioning items were displayed in the MARS-5 across gender, and the MARS-5 total score was strongly correlated with the MPR (r= 0.7). Multiple regression models showed that the MARS-5 and the MPR shared several similar determinants. In addition, the variance of the MARS-5 (R2= 0.567) was more than that of the MPR (R2= 0.300).

Conclusions:

The MARS-5 is a feasible and valid self-assessed medication adherence for older patients with stroke. In addition, several determinants were found to be related to medication adherence for older patients with stroke. Healthcare providers may want to take heed of these determinants to improve medication adherence for this population.
Risk of Anal Cancer in Women With a Human Papillomavirus–Related Gynecological Neoplasm: Puerto Rico 1987–2013
Authors: Acevedo-Fontánez Adrianna I. , Suárez Erick , Torres Cintrón Carlos R. , Ortiz Ana P.
Published: April 2018

Objective

The aim of the study was to estimate the magnitude of the association between HPV-related gynecological neoplasms and secondary anal cancer among women in Puerto Rico (PR).

Materials and Methods

We identified 9,489 women who had been diagnosed with a primary cervical, vaginal, or vulvar tumor during 1987–2013. To describe the trends of invasive cervical, vulvar, vaginal, and anal cancer, the age-adjusted incidence rates were estimated using the direct method (2000 US as Standard Population). Standardized incidence ratios (observed/expected) were computed using the indirect method; expected cases were calculated using 2 methods based on age-specific rates of anal cancer in PR. The ratio of standardized incidence ratios of anal cancer was estimated using the Poisson regression model to estimate the magnitude of the association between HPV-gynecologic neoplasms and secondary anal cancer.

Results

A significant increase in the incidence trend for anal cancer was observed from 1987 to 2013 (annual percent change = 1.1, p < .05), whereas from 2004 to 2013, an increase was observed for cervical cancer incidence (annual percent change = 3.3, p < .05). The risk of secondary anal cancer among women with HPV-related gynecological cancers was approximately 3 times this risk among women with non–HPV-related gynecological cancers (relative risk = 3.27, 95% CI = 1.37 to 7.79).

Conclusions

Anal cancer is increasing among women in PR. Women with gynecological HPV-related tumors are at higher risk of secondary anal cancer as compared with women from the general population and with those with non–HPV-related gynecological cancers. Appropriate anal cancer screening guidelines for high-risk populations are needed, including women with HPV-related gynecological malignancies and potentially other cancer survivors.
Ganoderma lucidum Polysaccharide Peptide Attenuates Skin Flap Ischemia-Reperfusion Injury in a Thioredoxin-Dependent Manner
Authors: Ren Huiwen , Meng Xiangbo , Yin Jian , Sun Jingyan , Huang Qingfeng , Yin Zhuming
Published: April 2018

Background:

Thioredoxin-1 plays an important role in protecting the skin flap from ischemia-reperfusion injury. Ganoderma lucidum polysaccharide peptide is the major component of G. lucidum, which possesses potent antioxidant and antiapoptotic activity. This study aims to determine whether G. lucidum polysaccharide peptide could attenuate skin flap ischemia-reperfusion injury and to investigate possible mechanisms involved.

Methods:

G. lucidum polysaccharide peptide was administered to mice and epidermal cells before ischemia-reperfusion and hypoxia/reoxygenation, respectively. The thioredoxin-1 inhibitor PX-12 was introduced in the counterevidence group. The flap tissues and cells were tested by hematoxylin and eosin and immunohistochemistry staining, terminal deoxynucleotidyl transferase-mediated dUDP end-labeling assay, superoxide dismutase and malonic dialdehyde measurement, and Western blot.

Results:

The survival rates of ischemia-reperfusion flaps and hypoxia/reoxygenation cells increased significantly following G. lucidum polysaccharide peptide treatment. Mitigated tissue damage, reduced apoptosis, and enhanced antioxidant activity were observed in ischemia-reperfusion flaps replenishing G. lucidum polysaccharide peptide. Western blot analysis revealed thioredoxin-1 depletion and a remarkable increase in ASK-1, phospho-p38, cleaved caspase-3, and cleaved PARP abundance in ischemia-reperfusion flaps and hypoxia/reoxygenation cells, whereas G. lucidum polysaccharide peptide dramatically up-regulated thioredoxin-1 and reduced the apoptosis-related protein expression. However, the rescue effect of G. lucidum polysaccharide peptide was notably blunted by supplementation with PX-12.

Conclusions:

The current investigation highlights the protective role of G. lucidum polysaccharide peptide in skin flap ischemia-reperfusion injury through a thioredoxin-1–dependent antioxidant and antiapoptotic pathway. This initial foray demonstrates the therapeutic value of G. lucidum polysaccharide peptide against ischemia-reperfusion and facilitates the understanding of its dermoprotective mechanism.
Anatomical Consideration for the Safe Elevation of the Deep Circumflex Iliac Artery in Flap Surgery
Authors: Shin Kang-Jae , Lee Shin-Hyo , Koh Ki-Seok , Song Wu-Chul
Published: April 2018

Background:

Deep circumflex iliac artery osteocutaneous flap transfer has frequently been applied to large defects in the maxillary and mandible regions, but the use rate has decreased gradually because of the complicated anatomy of the deep circumflex iliac artery. This study investigated the comprehensive anatomy of the deep circumflex iliac artery in relation to flap surgery with the aim of providing navigational guidelines for safe deep circumflex iliac artery harvesting.

Methods:

Sixty-two sides of the hemi–abdominal wall were dissected in fixed Korean cadavers. Several dimensions of the deep circumflex iliac artery and its positional relationships with surgical landmarks were measured, and the patterns of the arterial supply and anastomosis were identified.

Results:

The mean distance between the anterior superior iliac spine and the lateral border of the femoral artery was 57.5 mm. The deep circumflex iliac artery generally originated almost at the same level as the inguinal ligament, and its highest level was 14.8 mm superior to that ligament. Emerging points of the ascending branch were observed both medial and lateral to the anterior superior iliac spine, but no transverse branch pierced the transversus abdominis muscle medial to the anterior superior iliac spine.

Conclusions:

The incision line for safe deep circumflex iliac artery harvesting was parallel and 2 cm superior to the inguinal ligament and 6 cm from the anterior superior iliac spine. This position of the safe incision line can be easily determined using the thumb. Sex differences in the incidence of the deep circumflex iliac artery originating above or below the inguinal ligament will be another useful guide for easily detecting the deep circumflex iliac artery.
Topical Aloe Vera Gel for Accelerated Wound Healing of Split-Thickness Skin Graft Donor Sites: A Double-Blind, Randomized, Controlled Trial and Systematic Review
Authors: Burusapat Chairat , Supawan Monlada , Pruksapong Chatchai , Pitiseree Anont , Suwantemee Chaichoompol
Published: April 2018

Background:

Aloe vera has been used to treat wounds since ancient times. However, data regarding the efficacy of aloe vera for burns and split-thickness skin graft donor sites are inconclusive.

Methods:

A double-blind, randomized, controlled trial was conducted. Patients who underwent split-thickness skin graft harvesting from the thigh were included. Split-thickness skin graft donor sites were divided into two groups: the aloe vera group and the placebo group. The visual analogue scale score was used to evaluate pain, and complete epithelialization was assessed. The authors searched electronic databases and included only international clinical trials published in the English language.

Results:

Twelve patients with 24 donor sites participated. Times to complete epithelization for the aloe vera and placebo groups were 11.5 ± 1.45 and 13.67 ± 1.61 days, respectively (p < 0.05). Visual analogue scale scores after wound dressing for the aloe vera and placebo groups were 17.18 ± 13.17 and 18.63 ± 11.20, respectively. No statistical significance was found between groups. Five articles met the inclusion criteria: four involved burns and one involved split-thickness skin graft donor sites. Three studies of burn wounds demonstrated improved epithelization and one did not. The split-thickness skin graft donor-site study indicated that wound healing time for the control group was significantly different from that of the aloe vera and placebo groups. The healing rate was not statistically different between groups.

Conclusion:

Topical aloe vera gel significantly demonstrated accelerated split-thickness skin graft donor-site healing but did not show significant pain relief.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, I.
Incomplete Facial Paralysis: The Use of the Ipsilateral Residual Facial Nerve as a Donor Nerve for Facial Reanimation
Authors: Gur Eyal , Zuker Ron M. , Zaretski Arik , Leshem David , Barnea Yoav , Arad Ehud , Yanko Ravit , Meilik Benjamin , Kedar Daniel J. , Fliss Ehud
Published: April 2018

Background:

The reconstructive approach for incomplete facial paralysis is not yet determined. In this article, the authors present a new surgical approach for patients with incomplete facial paralysis in which residual, ineffective movement is detected preoperatively in the ipsilateral buccozygomatic territory of the paretic facial nerve.

Methods:

Sixteen patients with incomplete facial paralysis were found eligible for the procedure and underwent one-stage facial reanimation performed by the senior author (E.G.). Reanimation was performed using free gracilis muscle transfer with neural coaptation to an active facial nerve branch(es) responsible for the predetected buccozygomatic residual movement. Patients were reviewed in a systematic fashion using a combined still photographic and video scoring scale for symmetry at rest and at dynamic states.

Results:

Following surgery, improved symmetry was observed in the majority of observations of the mouth region at rest and while smiling and of the nasolabial fold region while smiling. There was no significant change in symmetry in the majority of observations of the eye region at rest and while smiling and the nasolabial fold region at rest. Video assessment of dynamic facial symmetry while smiling demonstrated improved symmetry in 91 percent of the observations (n = 191 observations). Comparison of mean scores for dynamic smile symmetry produced a statistically significant improvement of 1.68 points following surgery (p < 0.001).

Conclusion:

Based on this series, the authors recommend that use of the ipsilateral facial nerve buccozygomatic residual branch be considered as a donor nerve for facial reanimation using a free gracilis muscle transfer in patients with incomplete facial paralysis with residual preoperative movement in the midface.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Association Between Alexithymia and Risk of Incident Cardiovascular Diseases in the SUpplémentation en VItamines et Minéraux AntioXydants (SU.VI.MAX) Cohort
Authors: Wiernik Emmanuel , Lemogne Cédric , Fezeu Léopold , Arnault Nathalie , Hercberg Serge , Kesse-Guyot Emmanuelle , Galan Pilar
Published: April 2018

Objective

Although it has been suggested that alexythymia is associated with cardiovascular diseases, studies are scarce and a causal relationship is questionable. This study explored the prospective association between alexithymia and cardiovascular events in middle-aged participants without cardiovascular history at baseline.

Methods

The 26-item Toronto Alexithymia Scale (TAS-26) was completed by 5586 participants of the French SUpplémentation en VItamines et Minéraux AntioXydants cohort (41.4% of men, M [SD] age = 52.2 [6.3] years) in 1996–1997. Covariates measured at baseline included age, occupational status, depressive symptoms, smoking status, body mass index, hypertension, diabetes, hypercholesterolemia, and hypertriglyceridemia. The follow-up ran from January 1, 1998, to the date of the first cardiovascular event, the date of death or September 1, 2007, whichever occurred first. Cardiovascular events were validated by an independent expert committee. Hazard ratios and 95% confidence intervals were computed with Cox regressions.

Results

During an average of 8.9 years of follow-up, 171 first cardiovascular events were validated. After adjustment for age, sex, and occupational status, there was no association between baseline alexithymia and cardiovascular events at follow-up (hazard ratio [95% confidence interval] for 15 points of TAS-26 = 1.00 [0.81–1.23], p > .99). Adjusting for all covariates, using binary TAS-26 cut-offs or TAS-26 subscores yielded similar nonsignificant results.

Conclusions

In this large prospective study, alexithymia and cardiovascular events were not associated among a nonclinical population. This casts some doubt on whether alexithymia could be a meaningful target in the prevention of cardiovascular diseases.

Clinical Trial Registration

Clinicaltrials.gov (NCT00272428).
Septic cutaneous emboli revealing a severe case of Klebsiella pneumoniae liver abscess syndrome
Authors: Paraschiv Florentina , Popescu Gabriel Adrian , Borcan Alina Maria
Published: April 2018

Introduction.
Klebsiella pneumoniae liver abscess syndrome (KLAS) is characterized by bacteraemia, liver abscesses and metastatic infection caused by a hypervirulent strain of Klebsiella pneumoniae, usually belonging to the capsular serotype K1 or K2. Initially, KLAS was described in Eastern Asia; recently isolated cases have been reported from different parts of the world.

Case presentation. We describe the case of a woman with KLAS including meningeal, ocular and cutaneous metastatic infection and organ dysfunctions (coagulation abnormalities, thrombocytopenia and increased creatinine level). The identification of a hypermucoviscous strain of Klebsiella pneumoniae was possible by culture from one of the cutaneous emboli and subsequently confirmed by blood cultures. The patient fully recovered after abscess drainage and prolonged antibiotic treatment.

Conclusion. We have pointed out about the importance of sampling each septic focus in order to identify the aetiology of a disseminate infection.
Mercury methylating microbial communities of boreal forest soils
Authors: Xu Jingying , Buck Moritz , Eklöf Karin , Osman Omneya , Schaefer Jeffra K. , Bishop Kevin , Björn Erik , Skyllberg Ulf , Bertilsson Stefan , Bravo Andrea G.
Published: April 2018

The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase,hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. ThehgcAsequences obtained were distributed among diverse clades, includingProteobacteria, Firmicutes, andMethanomicrobia,withDeltaproteobacteria, particularlyGeobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is linked to the composition of also non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for thehgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.

Importance

Despite a global state of awareness that mercury, and methylmercury in particular, is a neurotoxin that millions of people continue to be exposed to, there are sizable gaps in our fundamental understanding of the processes and organisms involved in methylmercury formation. In the present study we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal forest soils. All the microorganisms identified have a relevant role on the processing of organic matter in soils. Moreover, our results show that the formation of methylation formation is not only linked to mercury methylating microorganisms but also to the presence of non-mercury methylating bacterial communities that contribute to methylmercury formation by the appropriate substrate to the microorganisms responsible for the actual methylation process. This study improves current knowledge on the diversity of organisms involved in methylmercury formation in soils.
Multilayer view of pathogenic SNVs in human interactome throughin-silicoedgetic profiling
Authors: Cui Hongzhu , Zhao Nan , Korkin Dmitry
Published: April 2018

Non-synonymous mutations linked to the complex diseases often have a global impact on a biological system, affecting large biomolecular networks and pathways. However, the magnitude of the mutation-driven effects on the macromolecular network is yet to be fully explored. In this work, we present an systematic multi-level characterization of human mutations associated with genetic disorders by determining their individual and combined interaction-rewiring, “edgetic”, effects on the human interactome. Ourin-silicoanalysis highlights the intrinsic differences and important similarities between the pathogenic single nucleotide variants (SNVs) and frameshift mutations. We show that pathogenic SNVs are more likely to cause gene pleiotropy than pathogenic frameshift mutations and are enriched on the protein interaction interfaces. Functional profiling of SNVs indicates widespread disruption of the protein-protein interactions and synergistic effects of SNVs. The coverage of our approach is several times greater than the recently published experimental study and has the minimal overlap with it, while the distributions of determined edgotypes between the two sets of profiled mutations are remarkably similar. Case studies reveal the central role of interaction-disrupting mutations in type 2 diabetes mellitus, and suggest the importance of studying mutations that abnormally strengthen the protein interactions in cancer. With the advancement of next-generation sequencing technology that drives precision medicine, there is an increasing demand in understanding the changes in molecular mechanisms caused by the patient-specific genetic variation. The current and futurein-silicoedgotyping tools present a cheap and fast solution to deal with the rapidly growing datasets of discovered mutations.
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats
Authors: Schmid Michael , Frei Daniel , Patrignani Andrea , Schlapbach Ralph , Frey Jürg E. , Remus-Emsermann Mitja N.P. , Ahrens Christian H.
Published: April 2018

Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length. Beyond long repeats, the P19E3 assembly was further complicated by a shufflon region. Its complex genome could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from the Oxford Nanopore Technology. Another important factor for a full genomic resolution was the choice of assembly algorithm.

Importantly, a repeat analysis indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this dark matter for de novo genome assembly of prokaryotes. Several of these dark matter genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assemblers capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.
Evidence for multifactorial processes underlying phenotypic variation in bat visual opsins
Authors: Sadier Alexa , Davies Kalina T. J. , Yohe Laurel R. , Yun Kun , Donat Paul , Hedrick Brandon P. , Dumont Elizabeth R. , Dávalos Liliana M. , Rossiter Stephen J. , Sears Karen E.
Published: April 2018

Studies of opsin genes offer insights into the evolutionary history and molecular basis of vertebrate color vision, but most assume intact open reading frames equate to functional phenotypes. Despite known variation in opsin repertoires and associated visual phenotypes, the genetic basis of such patterns has not been examined at each step of the central dogma. By comparing sequences, gene expression, and protein localization across a hyperdiverse group of mammals, noctilionoid bats, we find evidence that independent losses of S-opsin arose through disruptions at different stages of protein synthesis, while maintenance relates to frugivory. Discordance between DNA, RNA, and protein reveals that the loss of short-wave sensitivity in some lineages resulted from transcriptional and post-transcriptional changes in addition to degradation of open reading frames. These mismatches imply that visual phenotypes cannot reliably be predicted from genotypes alone, and connect ecology to multiple mechanisms behind the loss of color in vertebrates.
Molecular mechanisms controlling the multistage post-translational processing of endogenous Nrf1α/TCF11 proteins to yield distinct proteoforms within the coupled positive and negative feedback circuits
Authors: Xiang Yuancai , Wang Meng , Hu Shaofan , Qiu Lu , Yang Fang , Zhang Zhengwen , Yu Siwang , Pi Jingbo , Zhang Yiguo
Published: April 2018

In an attempt to terminate the chaotic state of the literature on Nrf1/TCF11 with various confused molecular masses, we herein establish a generally acceptable criterion required for identification of its endogenous full-length proteins and derivative isoforms expressed differentially in distinct experimental cell lines. Further work has been focused on the molecular mechanisms that dictate the successive multistate post-translational modifications (i.e. glycosylation by OST, deglycosylation by NGLY, and ubiquitination by Hrd1) of this CNC-bZIP protein and its proteolytic processing to yield multiple isoforms. Several lines of experimental evidence have demonstrated that the nascent Nrf1α/TCF11 polypeptide (non-glycosylated) is transiently translocated into the endoplasmic reticulum (ER), in which it becomes an inactive glycoprotein-A, and also folded in a proper topology within and around membranes. Thereafter, dynamic repositioning of the ER-resident domains in Nrf1 glycoprotein is driven by p97-fueled retrotranslocation into extra-ER compartments. Therein, glycoprotein of Nrf1 is allowed for digestion into a deglycoprotein-B and then its progressive proteolytic processing by cytosolic DDI-1/2 and proteasomes to yield distinct proteoforms (i.e. protein-C/D). The processing is accompanied by removal of a major N-terminal ~12.5-kDa polypeptide from Nrf1α. Interestingly, our present study has further unraveled that coupled positive and negative feedback circuits exist between Nrf1 and its cognate target genes, including those encoding its regulators p97, Hrd1, DDI-1 and proteasomes. These key players are differentially or even oppositely involved in diverse cellular signalling responses to distinct extents of ER-derived proteotoxic and oxidative stresses induced by different concentrations of proteasomal inhibitors.
Direct RNA Sequencing of the Complete Influenza A Virus Genome
Authors: Keller Matthew W. , Rambo-Martin Benjamin L. , Wilson Malania M. , Ridenour Callie A. , Shepard Samuel S. , Stark Thomas J. , Neuhaus Elizabeth B. , Dugan Vivien G. , Wentworth David E. , Barnes John R.
Published: April 2018

For the first time, a complete genome of an RNA virus has been sequenced in its original form. Previously, RNA was sequenced by the chemical degradation of radiolabelled RNA, a difficult method that produced only short sequences. Instead, RNA has usually been sequenced indirectly by copying it into cDNA, which is often amplified to dsDNA by PCR and subsequently analyzed using a variety of DNA sequencing methods. We designed an adapter to short highly conserved termini of the influenza virus genome to target the (-) sense RNA into a protein nanopore on the Oxford Nanopore MinION sequencing platform. Utilizing this method and total RNA extracted from the allantoic fluid of infected chicken eggs, we demonstrate successful sequencing of the complete influenza virus genome with 100% nucleotide coverage, 99% consensus identity, and 99% of reads mapped to influenza. By utilizing the same methodology we can redesign the adapter in order to expand the targets to include viral mRNA and (+) sense cRNA, which are essential to the viral life cycle. This has the potential to identify and quantify splice variants and base modifications, which are not practically measurable with current methods.
Visual reconstruction from 2-photon calcium imaging suggests linear readout properties of neurons in mouse primary visual cortex
Authors: Garasto Stef , Bharath Anil A. , Schultz Simon R.
Published: April 2018

Deciphering the neural code, that is interpreting the responses of sensory neurons from the perspective of a downstream population, is an important step towards understanding how the brain processes sensory stimulation. While previous work has focused on classification algorithms to identify the most likely stimulus label in a predefined set of categories, fewer studies have approached a full stimulus reconstruction task. Outstanding questions revolve around the type of algorithm that is most suited to decoding (i.e. full reconstruction, in the context of this study), especially in the presence of strong encoding non-linearities, and the possible role of pairwise correlations. We present, here, the first pixel-by-pixel reconstruction of a complex natural stimulus from 2-photon calcium imaging responses of mouse primary visual cortex (V1). We decoded the activity of approximately 100 neurons from layer 2/3 using an optimal linear estimator and an artificial neural network. We also investigated how much accuracy is lost in this decoding operation when ignoring pairwise neural correlations. We found that a simple linear estimator is sufficient to extract relevant stimulus features from the neural responses, and that it was not significantly outperformed by a non-linear decoding algorithm. The importance of pairwise correlations for reconstruction accuracy was also limited. The results of this study suggest that, conditional on the spatial and temporal limits of the recording technique, V1 neurons display linear readout properties, with low information content in the joint distribution of their activity.
Precise detection of S phase onset reveals decoupled G1/S transition events
Authors: Grant Gavin D. , Kedziora Katarzyna M. , Limas Juanita C. , Purvis Jeremy E. , Cook Jeanette Gowen
Published: April 2018

The eukaryotic cell division cycle is the process by which cells duplicate their genomes and proliferate. Transitions between sequential cell cycle phases are tightly orchestrated to ensure precise and efficient cell cycle progression. Interrogating molecular events at these transitions is important for understanding normal and pathological cell proliferation and mechanisms that ensure genome stability. A popular fluorescent reporter system known as “FUCCI” has been widely adopted for identifying cell cycle phases. Using time-lapse fluorescence microscopy, we quantitatively analyzed the dynamics of the FUCCI reporters relative to the transitions into and out of S phase. Although the original reporters reflect the E3 ubiquitin ligase activities for which they were designed, SCFSkp2 and APCCdh1, their dynamics are significantly and variably offset from actual S phase boundaries. To precisely mark these transitions, we generated and thoroughly validated a new reporter containing a PCNA-interacting protein degron whose oscillations are directly coupled to the process of DNA replication itself. We combined this reporter with the geminin-based APCCdh1 reporter to create “PIP-FUCCI.” PIP degron reporter dynamics closely correlate with S phase transitions irrespective of reporter expression levels. Using PIP-FUCCI, we made the unexpected observation that the apparent timing of APCCdh1 inactivation frequently varies relative to the onset of S phase. We demonstrate that APCCdh1 inactivation is not a strict pre-requisite for S phase entry, though delayed APCCdh1 inactivation correlates with longer S phase. Our results illustrate the benefits of precise delineation of cell cycle phase boundaries for uncovering the sequences of molecular events at critical cell cycle transitions.
Translation elongation and mRNA stability are coupled through the ribosomal A-site
Authors: Hanson Gavin , Alhusaini Najwa , Morris Nathan , Sweet Thomas , Coller Jeff
Published: April 2018

Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in eukaryotic cells. Previous work by us and others has shown that codon identity exerts a powerful influence on mRNA stability. InSaccharomyces cerevisiae, studies using a handful of reporter mRNAs show that optimal codons increase translation elongation rate, which in turn increase mRNA stability. However, a direct link between elongation rate and mRNA stability has not been established across the entire yeast transcriptome. In addition, there is evidence from work in higher eukaryotes that amino acid identity influences mRNA stability, raising the question as to whether the impact of translation elongation on mRNA decay is at the level of tRNA decoding, amino acid incorporation, or some combination of each. To address these questions, we performed ribosome profiling of wildtype yeast. In good agreement with other studies, our data showed faster codon-specific elongation over optimal codons and faster transcript-level elongation correlating with transcript optimality. At both the codon-level and transcript-level, faster elongation correlated with increased mRNA stability. These findings were reinforced by showing increased translation efficiency and kinetics for a panel of 11HIS3reporter mRNAs of increasing codon optimality. While we did observe that elongation measured by ribosome profiling is composed of both amino acid identity and synonymous codon effects, further analyses of these data establish that A-site tRNA decoding rather than other steps of translation elongation is driving mRNA decay in yeast.
RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome
Authors: Chen Weizhong , Yan Zhangming , Li Simin , Huang Norman , Huang Xuerui , Zhang Jin , Zhong Sheng
Published: April 2018

Nuclear speckles are interchromatin structures enriched in RNA splicing factors. Determining their relative positions with respect to the folded nuclear genome could provide critical information on co-and post-transcriptional regulation of gene expression. However, it remains challenging to identify which parts of the nuclear genome are in proximity to nuclear speckles, due to physical separation between nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNAs, 7SK and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA,nuclearspeckleassociated RNA), may extend to sufficient proximity to the nuclear genome. Leveraging a transcriptome-genome interaction assay (MARGI), we identified nsaRNA-interacting genomic sequences, which exhibited clustering patterns (nsaPeaks) in the genome, suggesting existence of relatively stable interaction sites for nsaRNAs in nuclear genome. Posttranscriptional pre-mRNAs, which are known to be clustered to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Furthermore, CDK9 proteins that localize to the vicinity of nuclear speckles produced ChIP-seq peaks that overlapped with nsaPeaks. Our combined DNA FISH and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs locate in sufficient proximity to nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.
Insights into centriole biogenesis and evolution revealed by cryoTomography of doublet and triplet centrioles
Authors: Greenan G. , Keszthelyi B. , Vale R. D. , Agard D. A.
Published: April 2018

Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) andDrosophila(doublet) centrioles at 25 Å resolution. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme.Drosophilacentrioles more closely resemble the mammalian core, but with their doublets linked through A tubules. The commonality of core region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.
HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo
Authors: Howard Jonathan M. , Lin Hai , Wallace Andrew J. , Kim Garam , Draper Jolene M. , Haeussler Maximilian , Katzman Sol , Toloue Masoud , Liu Yunlong , Sanford Jeremy R.
Published: April 2018

Alternative pre-mRNA splicing plays a major role in expanding the transcript output of human genes. This process is regulated, in part, by the interplay of trans-acting RNA binding proteins (RBPs) with myriad cis-regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein-coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on noncoding regions (introns). One of the earliest events in this process is recognition of the 3′ splice site (3′ss) by U2 small nuclear RNA auxiliary factor 2 (U2AF2). Splicing regulators, such as the heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), influence spliceosome assembly both in vitro and in vivo, but their mechanisms of action remain poorly described on a global scale. HNRNPA1 also promotes proofreading of 3′ss sequences though a direct interaction with the U2AF heterodimer. To determine how HNRNPA1 regulates U2AF–RNA interactions in vivo, we analyzed U2AF2 RNA binding specificity using individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) in control and HNRNPA1 overexpression cells. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3′ss of alternative cassette exons but not constitutive exons upon HNRNPA1 overexpression. A subset of these events shows a concomitant increase of U2AF2 crosslinking at distal intronic regions, suggesting a shift of U2AF2 to “decoy” binding sites. Of the many noncanonical U2AF2 binding sites, Alu-derived RNA sequences represented one of the most abundant classes of HNRNPA1-dependent decoys. We propose that one way HNRNPA1 regulates exon definition is to modulate the interaction of U2AF2 with decoy or bona fide 3′ss.