bluuebunny/crossref_metadata_2025 huggingface dataset:
Catechol-O-Methyltransferase (COMT) rs4680 Val158Met Polymorphism is Associated With Widespread Pressure Pain Sensitivity and Depression in Women With Chronic, but not Episodic, Tension-Type Headache
Authors: Fernández-de-las-Peñas César , Ambite-Quesada Silvia , Palacios-Ceña María , Guillem-Mesado Amparo , Guerrero-Peral Ángel , Pareja Juan A. , Arendt-Nielsen Lars
Published: January 2019

Objectives:

The aims of this study were: (1) to investigate the association between the rs4680
Val158Met polymorphism in frequent episodic tension-type headache (FETTH) and chronic tension-type headache (CTTH); and (2) to analyze the association between the rs4680
Val158Met polymorphism with clinical, psychological, or psychophysical variables.

Methods:

In total, 50 women with FETTH, 50 with CTTH, and 50 matched headache-free women participated. After amplifying Val158Met polymorphism by polymerase chain reaction, the genotype frequencies and allele distributions based on restriction fragment length polymorphism were assessed. Participants were classified according to the Val158Met polymorphism
rs4680 genotype (Val/Val, Val/Met, or Met/Met). A headache diary collected clinical features. Disability (Headache Disability Inventory), sleep quality (Pittsburgh Sleep Quality Index), and depression/anxiety levels (Hospital Anxiety and Depression Scale) were also assessed. Pressure pain thresholds were assessed bilaterally over the temporalis, upper trapezius, second metacarpal, and tibialis anterior by a blinded assessor.

Results:

The distribution of rs4680 Val158Met genotype was not significantly different between women with/without headache (P=0.796). No differences in headache features, disability, anxiety, or sleep quality were observed depending on the rs4680 Val158Met genotype. Women with CTTH, but not FETTH, carrying the Met/Met genotype had lower widespread pressure pain thresholds and higher depressive symptoms than those with Val/Val or Val/Met genotype (P<0.05).

Conclusions:

The Val158Met polymorphism (rs4680) does not appear to be involved in predisposition to tension-type headache; however, this genetic factor may be involved in the pathogenesis expression of CTTH, as greater pressure pain sensitivity and higher depressive levels were found in CTTH carrying the Met/Met genotype.
Surgical Gowning Technique: Are We Contaminated Before We Cut?
Authors: Panas Kenton , Wojcik Jonathan , Falcon Spencer , Hollabaugh Kimberly , Hickerson Lindsay E.
Published: January 2019

Objectives:

To assess possible breaches of sterility during the initial gowning step.

Design:

Observational study. Twenty-seven gowning events were monitored for contamination during a simulated two-person gowning process in which a surgical technician assists a surgeon in the gowning process at the beginning of a surgical procedure. The lower portion of the technician's gown was coated with resin powder before the gowning process to simulate contamination.

Setting:

Single-institution Level 1 trauma center.

Participants:

Three physicians and 3 tenured surgical technicians.

Intervention:

Observed contaminated areas represented by ultraviolet resin powder under ultraviolet light on the gown of the surgeon after the two-person gowning step.

Main Outcome Measurement:

Number and surface area of contamination events.

Results:

There was a 66.67% rate of contamination of the surgeon's gown sleeves while being gowned by a surgical technician. The overall median contamination for the short surgeon was 1.3 cm2. For the medium height surgeon, the overall median contamination was 1.4 cm2. The tall surgeon had an overall median contamination of 2.9 cm2. Of the short, medium, and tall surgeons, the number of contamination events was 6, 5, and 7, respectively. The study suggested that the surgeon's height was a significant source of variation (P = 0.046).

Conclusion:

We present an observational pilot study that suggests that to reduce contamination in the operating room, the two-person method must be highly monitored. This study also proposes that the single-person gowning technique should be used to reduce contamination rate during the gowning process.
Expression of cancer/testis antigens in cutaneous melanoma: a systematic review
Authors: Tio Darryl , Kasiem Fazira R. , Willemsen Marcella , van Doorn Remco , van der Werf Nienke , Hoekzema Rick , Luiten Rosalie M. , Bekkenk Marcel W.
Published: January 2019

The cancer/testis antigen (CTA) family is a group of antigens whose expression is restricted to male germline cells of the testis and various malignancies. This expression pattern makes this group of antigens potential targets for immunotherapy. The aim of this study was to create an overview of CTA expressed by melanoma cells at mRNA and protein level. A systematic literature search was performed in Medline (PubMed) and Embase from inception up to and including February 2018. Studies were screened for eligibility by two independent reviewers. A total of 65 full-text articles were included in the final analysis. A total of 48 CTA have been studied in melanoma. Various CTA show different expression rates in primary and metastatic tumours. Of the 48 CTA, the most studied were MAGE-A3, MAGE-A1, NY-ESO-1, MAGE-A4, SSX2, MAGE-A2, MAGE-C1/CT7, SSX1, MAGE-C2/CT10 and MAGE-A12. On average, MAGE-A3 mRNA is present in 36% of primary tumours, whereas metastatic tumours have an expression rate of 55–81%. The same applies to the protein expression rate of MAGE-A3 in primary tumours, which is reported to be at 15–37%, whereas metastatic tumours have a higher expression rate of 25–70%. This trend of increased expression in metastases compared with primary tumours is observed with MAGE-A1, MAGE-A2, MAGE-A4, MAGE-A12 and NY-ESO-1. Many CTA are expressed on melanoma. This review provides an overview of the expression frequency of CTAs in melanoma and may aid in identifying CTA as the therapeutic target for immunotherapy.
Inositol hexaphosphate plus inositol induced complete remission in stage IV melanoma: a case report
Authors: Khurana Sharad , Baldeo Candice , Joseph Richard W.
Published: January 2019

Inositol hexaphosphate (IP6) also called phytic acid is a polyphosphorylated carbohydrate naturally found in cereals, nuts, grains, and high-fiber-containing foods. It has been shown to inhibit the growth of many different tumor cell lines both in vitro and in vivo like colon, pancreas, liver, prostate, and even melanoma. Vitamin B inositol is a precursor of IP6 and another naturally occurring compound with anticancer properties. We present a case report of a patient with metastatic melanoma who declined traditional therapy and opted to try over the counter supplement IP6+inositol instead. To our surprise, the patient achieved a complete remission and remains in remission 3 years later. On the basis of this case and previous preclinical studies, we believe further research is indicated in exploring antiproliferative and potential immune stimulating effects of IP6+inositol in patients with metastatic melanoma.
Anal Cancer Precursor Lesions in HIV-Infected Persons: Tissue Human Papillomavirus Type Distribution and Impact on Treatment Response
Authors: Kobayashi Takaaki , Sigel Keith , Kalir Tamara , MacLeod Iain J. , Liu Yuxin , Gaisa Michael
Published: January 2019

BACKGROUND:

Data on tissue distribution of human papillomavirus types in anal high-grade squamous intraepithelial lesions are limited and the impact on treatment outcomes poorly understood.

OBJECTIVE:

We aimed to investigate potential predictors of treatment failure after electrocautery ablation, including human papillomavirus type(s) isolated from index lesions.

DESIGN:

This was a retrospective cohort study.

SETTINGS:

The study was conducted at a tertiary academic referral center in New York City.

PATIENTS:

Seventy-nine HIV-infected patients with a diagnosis of anal high-grade squamous intraepithelial lesions between January 2009 and December 2012 were included, and genomic DNA was extracted from biopsy tissue.

MAIN OUTCOME MEASURES:

The prevalence of human papillomavirus types in index lesions and surveillance biopsies after electrocautery ablation were analyzed to evaluate treatment response.

RESULTS:

Of 79 anal high-grade squamous intraepithelial lesions, 71 (90%) tested positive for ≥1 human papillomavirus type; 8 (10%) had no human papillomavirus detected. The most common type was 16 (39%), followed by 33 (15%). Human papillomavirus type 18 was seen in 3%. Sixty-one patients (77%) underwent electrocautery ablation and had subsequent surveillance biopsies. Surveillance biopsies yielded benign findings or low-grade squamous intraepithelial lesions in 31 (51%) of 61 and recurrent high-grade squamous intraepithelial lesions in 30 (49%) of 61 patients (mean follow-up: 35 mo). Ablation response did not differ significantly based on baseline demographics, smoking history, history of anogenital warts, mean CD4+ T-cell count, antiretroviral-therapy use, and HIV viral load (<50 copies/mL). The recurrence of high-grade lesions was not significantly associated with high-risk human papillomavirus types detected in index lesions.

LIMITATIONS:

Human papillomavirus genotyping in surveillance biopsies was not performed.

CONCLUSIONS:

Anal high-grade squamous intraepithelial lesions in HIV-infected patients contain a wide range of human papillomavirus types, and individual lesions commonly harbor multiple types concomitantly. Recurrence of anal high-grade squamous intraepithelial lesions after electrocautery ablation occurs frequently and is not affected by high-risk human papillomavirus types. See Video Abstract at http://links.lww.com/DCR/A833.
Use of Eye Shields for Mohs Micrographic Surgery of the Eyelids and Periorbital Area
Authors: Shih Shawn , Khachemoune Amor
Published: January 2019

BACKGROUND

Internal eye shields are designed for use in periorbital procedures, but their use in Mohs micrographic surgery (MMS) of the eyelids has rarely been reported in the literature.

OBJECTIVE

The authors aim to discuss different types of internal eye shields as well as their indication, proper use, and potential complications.

MATERIALS AND METHODS

The authors performed a literature search on PubMed with the keywords “internal eye shield,” “corneal shield,” “scleral shield,” and “periorbital Mohs micrographic surgery” with no restriction on publication time frame due to the scarcity of relevant literature.

RESULTS

Experts seem to agree that use of eye shield for MMS of the eyelids is a reasonable measure to undertake to prevent operative injuries. Although either plastic or stainless steel eye shield can be used, plastic eye shields are often preferred and recommended in procedures where electrosurgical devices need to be used.

CONCLUSION

Although the authors recommend the use of internal eye shields for MMS of the eyelids for preventing operative injuries, this recommendation (Grade C) is based on very limited evidence (Level 5). More research and higher-powered studies are needed for conclusive evidence and to establish clear guidelines for providers.
Simultaneous Lateral Tarsal Strip and Medial Spindle Procedures for Cicatricial Ectropion
Authors: Goddard Lindsey , Chesnut Cameron
Published: January 2019

BACKGROUND

Lateral tarsal strip (LTS) and medial spindle (MS) procedures are surgical techniques used to address cicatricial ectropion.

OBJECTIVE

To evaluate the clinical characteristics and efficacy of simultaneous LTS and MS procedures for repair of cicatricial ectropion occurring after dermatologic surgeries.

METHODS

A retrospective review of all cases of symptomatic, cicatricial, lateral, and medial punctal ectropion in 1 author's (C.C.) practice over 2 years was performed. Those resulting from dermatologic surgical procedures and repaired with simultaneous LTS and MS procedures were included.

RESULTS

Fifty-six tumors involving the lower eyelid were considered highly at risk and treated with Mohs micrographic surgery and reconstruction in the senior author's practice during the review period, resulting in 3 (5.3%) cases of cicatricial ectropion. Five additional cases resulted from Mohs surgery and 7 resulted from excisions of pigmented lesions, all performed by other surgeons. One postoperative complication (6.7%) of undercorrection required reoperation, with initial surgical success rate being 93.3% and overall surgical success being 100% after the single reoperation.

CONCLUSION

Simultaneous LTS and MS are useful procedures for dermatologic surgeons yielding high surgical success and a low complication rate for correction of medial and lateral cicatricial ectropion with punctal eversion.
When Preoperative Imaging and Audiometry Conflict: A Case of Cochlear Implantation in a Prelingually Deafened Adult
Authors: Raymond Mallory , Vivas Esther X.
Published: January 2019

Objective:

To describe a unique case of excellent audiometric outcomes for a prelingually deafened adult after cochlear implantation and to caution on the limits of magnetic resonance imaging for a diagnosis of cochlear nerve aplasia.

Patient:

Adult man with congenital bilateral profound sensorineural hearing loss.

Intervention (s):

Cochlear implantation.

Main Outcome Measure(s):

Audiometric testing and subjective hearing improvement.

Results:

Improved subjective and objective hearing after cochlear implantation.

Conclusions:

Consideration of cochlear implantation is reasonable for adults with long-standing hearing loss when preoperative audiometric testing is discordant with magnetic resonance imaging findings of radiographic cochlear nerve aplasia.
Trends in Incidence and Outcomes of Clostridium difficile Colitis in Hospitalized Patients of Febrile Neutropenia
Authors: Siddiqui Nauman S. , Khan Zubair , Khan Mohammad S. , Khan Zarmina , Haq Khwaja F. , Solanki Shantanu D. , Munigala Satish , Khan Muhammad A. , Saif Muhammad W. , Nawras Ali
Published: January 2019

Introduction:

Clostridium difficile infection (CDI) has been attracting attention lately as the most common hospital acquired infection. Patients with neutropenia because of malignancy seem to be at an increased risk for developing CDI. There is currently limited data that assesses the national burden and outcomes of CDI in Febrile Neutropenia (FN).

Methods:

We analyzed the National Inpatient Sample (NIS) database for all subjects with discharge diagnosis of FN with or without CDI (ICD-9 codes 288.00, 288.03,780.60, and 008.45) as primary or secondary diagnosis during the period from 2008 to 2014. All analyses were performed with SAS, version 9.4 (SAS Institute).

Results:

From 2008 to 2014 there were total 19422 discharges of FN patients with CDI. There was a rising incidence of CDI in patients with FN from 4.11% (in 2008) to 5.83% (in 2014). The In-hospital mortality showed a decreasing trend from 7.79% (in 2008) to 5.32% (in 2014), likely because of improvements in diagnostics and treatment. The overall mortality (6.37% vs. 4.61%), length of stay >5 days (76.45% vs. 50.98%), hospital charges >50,000 dollars (64.43% vs. 40.29%), colectomy and colostomy (0.35% vs. 0.15%), and discharge to skilled nursing facility (10.47% vs. 6.43%) was significantly more in FN patients with CDI versus without CDI over 7 years (2008 to 2014). Age above 65 years, Hispanic race, hematological malignancies, urban hospital settings, and sepsis were significant predictors of mortality in febrile neutropenia patients with CDI.

Discussion:

Despite the significant decrease in mortality, the incidence of CDI is rising in hospitalized FN patients with underlying hematological malignancies. Risk factor modification, with the best possible empiric antibiotic regimen is imperative for reducing mortality and health care costs in this cohort.
Efficacy and Safety of Recombinant Activated Factor VII Off-label Use in a Pediatric Hematology/Oncology Cohort
Authors: Mesleh Shayeb Akram , Su Yin , Kang Guolian , Elbahlawan Lama , Reiss Ulrike M.
Published: January 2019

Background:

Recombinant activated factor VII (rFVIIa) has been used off-label to treat or prevent severe bleeding in patients for whom conventional treatments are unsuccessful. However, studies in children remain limited.

Procedure:

To examine the efficacy and safety of rFVIIa, we performed a retrospective analysis of rFVIIa off-label use in a pediatric hematology/oncology cohort at a single center from 2006 to 2014.

Results:

Of 58 patients identified, 46 (79.3%) received rFVIIa to treat bleeding and 12 (20.7%) to prevent bleeding. Thirty-three (71.7%) patients had life-threatening bleeding. In the treatment group, 63.0% patients were responders (ie, bleeding decreased or stopped) and 37.0% were nonresponders (ie, bleeding did not change). Blood products usage was similar between responders and nonresponders. After rFVIIa administration, prothrombin time, partial thromboplastin time and lactate were significantly lower, but fibrinogen was significantly higher in responders than nonresponders. Venous thromboembolism developed in 5.2% (3/58) patients, but its relation to rFVIIa remains unclear. Responders had significantly lower mortality than nonresponders (17.2% vs. 82.4%, P<0.0001).

Conclusions:

rFVIIa controlled most bleeding events in this cohort, despite predominance of life-threatening bleeding, suggesting good efficacy. Venous thromboembolism rate was low. Further studies are warranted to identify predictors of favorable response to rFVIIa in similar patients.
Hydronephrosis Associated With Pelvic Organ Prolapse: A Systematic Review
Authors: Siddique Moiuri , Ingraham Caitlin , Kudish Bela , Iglesia Cheryl B. , Polland Allison
Published: January 2019

Objectives

The aim of this study was to report the prevalence of hydronephrosis associated with pelvic organ prolapse (POP).

Methods

We conducted a MEDLINE and PubMed search from 1996 to October 2016 using PRISMA guidelines. Eight studies met criteria for inclusion, including 3 prospective and 5 retrospective studies.

Results

The prevalence of hydronephrosis ranged from 3.5% to 30.6% in studies that included multiple stages of prolapse. Hydronephrosis correlated with prolapse severity in multiple studies, but serum creatinine did not consistently predict hydronephrosis. Two studies reported a significantly higher prevalence of hydronephrosis in patients with uterovaginal prolapse compared with vaginal vault prolapse. Complete resolution of hydronephrosis was described in 56% to 83% of patients after undergoing surgical treatment for advanced prolapse.

Conclusions

Hydronephrosis among patients with POP is not rare, and we suggest consideration of upper tract evaluation in patients presenting with POP, particularly in those with advanced uterovaginal prolapse electing to proceed with expectant or conservative management.
High-throughput enrichment and isolation of megakaryocyte progenitor cells from the mouse bone marrow
Authors: Bush Lucas M. , Healy Connor P. , Marvin James E. , Deans Tara L.
Published: January 2019

Megakaryocytes are a rare population of cells that develop in the bone marrow and function to produce platelets that circulate throughout the body and form clots to stop or prevent bleeding. A major challenge in studying megakaryocyte development, and the diseases that arise from their dysfunction, is the identification, classification, and enrichment of megakaryocyte progenitor cells that are produced during hematopoiesis. Here, we present a high throughput strategy for identifying and isolating megakaryocytes and their progenitor cells from a heterogeneous population of bone marrow samples. Specifically, we couple thrombopoietin (TPO) induction, image flow cytometry, and principle components analysis (PCA) to identify and enrich for megakaryocyte progenitor cells that are capable of self-renewal and directly differentiating into mature megakaryocytes. This enrichment strategy distinguishes megakaryocyte progenitors from other lineage-committed cells in a high throughput manner. Furthermore, by using image flow cytometry with PCA, we have identified a combination of markers and characteristics that can be used to isolate megakaryocyte progenitor cells using standard flow cytometry methods. Altogether, these techniques enable the high throughput enrichment and isolation of cells in the megakaryocyte lineage and have the potential to enable rapid disease identification and diagnoses ahead of severe disease progression.
RNAIndel: discovering somatic coding indels from tumor RNA-Seq data
Authors: Hagiwara Kohei , Ding Liang , Edmonson Michael N. , Rice Stephen V. , Newman Scott , Meshinchi Soheil , Ries Rhonda E. , Rusch Michael , Zhang Jinghui
Published: January 2019

Reliable identification of expressed somatic insertion/deletion (indels) is an unmet demand due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor trasncriptome.

By implementing features characterized by PCR-free whole-genome and whole-exome sequencing into a machine-learning framework, we present RNAIndel, a tool for predicting somatic, germline and artifact indels from tumor RNA-Seq data alone. RNAIndel robustly predicts 87□93% of somatic indels from 235 samples with heterogeneous conditions, even recovering subclonal (VAF range 0.01–0.15) driver indels missed by targeted deep-sequencing, outperforming the current best-practice for RNA-Seq variant calling which had 57% sensitivity but with 12 times more false positives.

RNAIndel is freely available at https://github.com/stjude/RNAIndel

Contact

jinghui.zhang@stjude.org
Dissociating orexin-dependent and -independent functions of orexin neurons using novel orexin-Flp knock-in mice
Authors: Chowdhury Srikanta , Jung Hung Chi , Izawa Shuntaro , Inutsuka Ayumu , Kawamura Meiko , Kawashima Takashi , Bito Haruhiko , Imayoshi Itaru , Abe Manabu , Sakimura Kenji , Yamanaka Akihiro
Published: January 2019

Uninterrupted arousal is important for survival during threatening situations. Activation of orexin/hypocretin neurons is implicated in sustained arousal. However, orexin neurons produce and release orexin as well as several co-transmitters including dynorphin and glutamate. Thus, it is important to disambiguate orexin peptide-dependent and -independent physiological functions of orexin neurons. To attain this, we generated a novel orexin-flippase (Flp) knock-in (KI) mouse line. Crossing with Flp-reporter or Cre-expressing mice showed gene expression exclusively in orexin neurons. Histological studies confirmed that orexin was completely knock-out (KO) in KI/KI homozygous mice. Orexin neurons without orexin showed altered electrophysiological properties, as well as received decreased glutamatergic inputs. Selective chemogenetic activation revealed that both orexin and co-transmitters functioned to increase wakefulness, however, orexin was indispensable to promote sustained arousal. Surprisingly, activation of orexin neurons without orexin caused a significant increase in the total time spent in cataplexy. Taken together, orexin is essential to maintain basic membrane properties and input-output computation of orexin neurons, as well as to exert awake-sustaining aptitude of orexin neurons.
GABA neurons in the ventral tegmental area regulate non-rapid eye movement sleep in mice
Authors: Chowdhury Srikanta , Matsubara Takanori , Miyazaki Toh , Ono Daisuke , Abe Manabu , Sakimura Kenji , Yamanaka Akihiro
Published: January 2019

The daily sleep/wakefulness cycle is regulated by coordinated interactions between sleep- and wakefulness-regulating neural circuitry. However, the detailed neural circuitry mediating sleep is far from understood. Here, we found that glutamic acid decarboxylase 67 (Gad67)-positive GABAergic neurons in the ventral tegmental area (VTAGad67+) are a key regulator of non-rapid eye movement (NREM) sleep in mice. VTAGad67+ neurons project to multiple brain areas implicated in sleep/wakefulness regulation such as the lateral hypothalamus (LH) and dorsal raphe nucleus. Chemogenetic activation of VTAGad67+ neurons promoted NREM sleep with higher delta power whereas optogenetic inhibition of these neurons induced prompt arousal from NREM sleep under highly somnolescent conditions, but not during REM sleep. In vivo fiber photometry recordings revealed that VTAGad67+ neurons showed the highest population activity in NREM sleep and the lowest activity in REM sleep. Acute brain slice electrophysiology combined with optogenetics revealed that VTAGad67+ neurons directly innervate and inhibit wake-promoting orexin/hypocretin neurons in the LH by releasing GABA. Taken together, we reveal that VTAGad67+ neurons play a crucial role in the regulation of NREM sleep.
Indolergic receptors of the elephant mosquitoToxorhynchites amboinensis
Authors: Amir Dekel , Yakir Esther , Bohbot Jonathan D.
Published: January 2019

The conservation of the mosquito indolergic receptors across the Culicinae and Anophelinae mosquito lineages, which spans 200 million years of evolution, is a testament to the central role of indolic compounds in the biology of these insects. Indole and skatole have been associated with the detection of oviposition sites and animal hosts. To evaluate the potential ecological role of these two compounds, we have used a pharmacological approach to characterize homologs of the indolergic receptorsOr2and Or10in the non-hematophagous elephant mosquitoToxorhynchites amboinensis. We provide evidence that both receptors are narrowly tuned to indole and skatole like their counterparts from hematophagous mosquitoes. These findings indicate that indole and skatole are operating in a non-animal-host seeking context inToxorhynchitesand underscore the importance of understanding their roles in hematophagous mosquitoes.
Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine
Authors: Borgers Katlyn , Ou Jheng-Yang , Zheng Po-Xing , Tiels Petra , Van Hecke Annelies , Plets Evelyn , Michielsen Gitte , Festjens Nele , Callewaert Nico , Lin Yao-Cheng
Published: January 2019

Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence of BCG Danish 1331 (07/270), one of the WHO reference strains for BCG vaccines. We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of this vaccine strain.
Myosin Orientation in a Muscle Fiber Determined with High Angular Resolution Using Bifunctional Spin Labels
Authors: Savich Yahor , Binder Benjamin P. , Thompson Andrew R. , Thomas David D.
Published: January 2019

We have measured the orientation of the myosin light chain domain (lever arm) elements in demembranated muscle fibers by electron paramagnetic resonance (EPR), using a bifunctional spin label (BSL), with angular resolution of 4 degrees. Despite advances in X-ray crystallography and cryo-electron microscopy (cryo-EM), and fluorescence polarization, none of these techniques provide high-resolution structural information about the myosin light chain domain under ambient conditions in a muscle fiber. Two cysteines, 4 residues apart, were engineered on two α-helices in the myosin regulatory light chain (RLC), permitting stereoselective site-directed labeling with BSL. One labeled helix (helix E) is adjacent to the myosin lever arm, the other helix (helix B) is located farther apart from the motor domain beyond the “hinge” of the myosin. By exchanging BSL-labeled RLC onto oriented muscle fibers, we obtained EPR spectra that determined angular distributions of BSL with high resolution, which enabled the accurate determination of helix orientation of individual structural elements with respect to the muscle fiber axis. In the absence of ATP (rigor), each of the two labeled helices exhibited both ordered (σ ~ 9-11 degrees) and disordered (σ > 38 degrees) populations. We used these angles to determine the orientation of the myosin lever arm, concluding that the oriented population has lever arms that are perpendicular to the muscle fiber axis. This orientation is ~33 degrees different than predicted from a standard “lever arm down” model based on cryo-EM of actin decorated with isolated myosin heads, but it is compatible with fluorescence polarization and EM data obtained from muscle fibers. The addition of ATP, in the absence of Ca2+, shifted the orientation to a much more disordered distribution.

We used electron paramagnetic resonance to determine the orientation of elements within the myosin regulatory light chain in skinned skeletal muscle fibers. A bifunctional spin label provided sufficient resolution to detect an ordered population of lever arms perpendicular to actin.
The Effects of Alcohol and Cannabinoid Exposure during the Brain Growth Spurt on Behavioral Development in Rats
Authors: Breit Kristen R. , Zamudio Brandonn , Thomas Jennifer D.
Published: January 2019

Cannabis is the most commonly used illicit drug among pregnant women. Moreover, over half of pregnant women who are consuming cannabis are also consuming alcohol; however, the consequences of combined prenatal alcohol and cannabis exposure on fetal development are not well understood. The current study examined behavioral development following exposure to ethanol (EtOH) and/or CP-55,940 (CP), a cannabinoid receptor agonist. From postnatal days (PD) 4-9, a period of brain development equivalent to the third trimester, Sprague-Dawley rats received EtOH (5.25g/kg/day) or sham intubation, as well as CP (0.4 mg/kg/day) or vehicle. All subjects were tested on open field activity (PD 18-21), spatial learning (PD 40-46), and elevated plus maze (PD 30) tasks. Both EtOH and CP increased locomotor activity in the open field, and the combination produced more severe overactivity than either exposure alone. Similarly, increases in thigmotaxis in the Morris water maze were caused by either EtOH or CP alone, and were more severe with combined exposure, although only EtOH impaired spatial learning. Finally, developmental CP, but not EtOH, increased time spent in the open arms on the elevated plus maze. Overall, these data indicate that EtOH and CP produce some independent domain-specific effects, but many effects of EtOH and CP on behavior were additive. Importantly, these data suggest that combined prenatal exposure to alcohol and cannabis may be more damaging to the developing fetus, which has implications for the lives of affected individuals and families and also for establishing public health policy.
Cortical and Cardiovascular Regulation Support Adaptation to Ambient Sound Environment
Authors: Hao Yu , Gupta Disha , Sun Qiuyan , Yao Lin
Published: January 2019

Adaptation in complex biological systems is a consequence of sensitivity to environmental changes. We investigate how responses to unattended background sound changes are influenced by the interaction of external (pitch sequence context) and internal factors (biological regulation). Cortical responses (electroencephalograph Mismatch Negativity) demonstrated increased intensity and prolonged latency in unattended pitch changes in the context of the ascending pitch sequence compared with the descending pitch sequence. Moreover, ascending pitch context is associated with more activation of anterior cingula cortex and insula, suggesting arousal effect and internal regulation. However, the intensified and prolonged responses were supported by cortical and cardiovascular biomarkers for regulation respectively. These findings suggest that biological regulation may be associated with environmental context and play different roles in response sensitivity in terms of intensity and speed.
Genetic predisposition to mosaic Y chromosome loss in blood is associated with genomic instability in other tissues and susceptibility to non-haematological cancers
Authors: Thompson Deborah J. , Genovese Giulio , Halvardson Jonatan , Ulirsch Jacob C. , Wright Daniel J. , Terao Chikashi , Davidsson Olafur B. , Day Felix R. , Sulem Patrick , Jiang Yunxuan , Danielsson Marcus , Davies Hanna , Dennis Joe , Dunlop Malcolm G. , Easton Douglas F. , Fisher Victoria A. , Zink Florian , Houlston Richard S. , Ingelsson Martin , Kar Siddhartha , Kerrison Nicola D. , Kristjansson Ragnar P. , Li Rong , Loveday Chey , Mattisson Jonas , McCarroll Steven A. , Murakami Yoshinori , Murray Anna , Olszewski Pawel , Rychlicka-Buniowska Edyta , Scott Robert A. , Thorsteinsdottir Unnur , Tomlinson Ian , Moghadam Behrooz Torabi , Turnbull Clare , Wareham Nicholas J. , Gudbjartsson Daniel F. ,   INTEGRAL-ILCCO,   The Breast Cancer Association Consortium,   CIMBA,   The Endometrial Cancer Association Consortium,   The Ovarian Cancer Association Consortium,   The PRACTICAL Consortium,   The Kidney Cancer GWAS Meta-Analysis Project,   eQTLGen Consortium,   BIOS Consortium,   23andMe Research Team, Kamatani Yoichiro , Finucane Hilary K. , Hoffmann Eva R. , Jackson Steve P. , Stefansson Kari , Auton Adam , Ong Ken K. , Machiela Mitchell J. , Loh Po-Ru , Dumanski Jan P. , Chanock Stephen J. , Forsberg Lars A. , Perry John R. B.
Published: January 2019

Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism, yet our knowledge of the causes and consequences of this is limited. Using a newly developed approach, we estimate that 20% of the UK Biobank male population (N=205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes involved in cell-cycle regulation, cancer susceptibility, somatic drivers of tumour growth and cancer therapy targets. Genetic susceptibility to LOY is associated with non-haematological health outcomes in both men and women, supporting the hypothesis that clonal haematopoiesis is a biomarker of genome instability in other tissues. Single-cell RNA sequencing identifies dysregulated autosomal gene expression in leukocytes with LOY, providing insights into how LOY may confer cellular growth advantage. Collectively, these data highlight the utility of studying clonal mosaicism to uncover fundamental mechanisms underlying cancer and other ageing-related diseases.
Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism
Authors: Duarte Isabel , Huynen Martijn A.
Published: January 2019

Lateral gene transfer (also known as Horizontal Gene Transfer) is the transmission of genetic material between phylogenetically unrelated organisms. Previous studies have been showing the importance of this process for the evolution of unicellular eukaryotes, particularly those living in highly competitive niches such as the herbivore gut.

Pyromices sp. is an obligate anaerobic chytrid fungus that grows as a commensal organism in the gut of mammalian herbivores, possessing hydrogenosomes instead of mitochondria, producing hydrogen, and playing a key role in the digestion of plant cell wall material. These particular features make its genome particularly valuable for the study of the evolution and adaptation of unicellular eukaryotes to the cellulose-rich and anaerobic environment of the herbivore gut.

Here we performed a detailed large-scale lateral gene transfer (LGT) analysis of the genome from the chytrid fungus Piromyces sp. strain E2. For this we set out to elucidate (i) which proteins were likely transferred to its genome, (ii) from which bacterial donor species, and (iii) which functions were laterally acquired. Using sequence comparison and phylogenetic analyses, we have found 704 LGT candidates, representing nearly 5% of the Piromyces sp. orfeome (i.e. the complete set of open reading frames), mostly transferred from Firmicutes, Fibrobacteres, Bacteroidetes and Proteobacteria, closely following the microbial abundance reported for the herbivore gut. With respect to the functional analysis, the LGT candidate set includes proteins from 250 different orthologous groups, with a clear over-representation of genes belonging to the Carbohydrate Transport and Metabolism functional class. Finally, we performed a graph density analysis on the metabolic pathways formed by the LGT candidate proteins, showing that the acquired functions fit cohesively within Piromyces metabolic network, and are not randomly distributed within the global KEGG metabolic map. Overall, our study suggests that Piromyces’ adaptation to living anaerobically and in the a cellulose-rich environment has been undoubtedly fostered by the acquisition of foreign genes from bacterial neighbors, showing the global importance of such evolutionary mechanisms for successful eukaryotic thriving in such competitive environments.
The Crystal Structure of Klebsiella pneumoniae FeoA Reveals a Site For Protein-Protein Interactions
Authors: Linkous Richard O. , Sestok Alexandrea E. , Smith Aaron T.
Published: January 2019

In order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe2+) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via intercalations into a Leu zipper motif. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate the KpFeoA can assume both ‘open’ and ‘closed’ conformations, controlled by peptide binding. We propose a model in which a ‘C-shaped’ clamp along the FeoA surface mediates interactions with its partner protein, FeoB. These findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions, which could be exploited for future antibiotic developments.
Diazepam Accelerates GABAAR Synaptic Exchange and Alters Intracellular Trafficking
Authors: Lorenz-Guertin Joshua M. , Bambino Matthew J. , Das Sabyasachi , Weintraub Susan T. , Jacob Tija C.
Published: January 2019

Despite 50+ years of clinical use as anxiolytics, anti-convulsants, and sedative/hypnotic agents, the mechanisms underlying benzodiazepine (BZD) tolerance are poorly understood. BZDs potentiate the actions of gamma-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the adult brain, through positive allosteric modulation of γ2 subunit containing GABA type A receptors (GABAARs). Here we define key molecular events impacting γ2 GABAAR and the inhibitory synapse gephyrin scaffold following initial sustained BZD exposure in vitro and in vivo. Using immunofluorescence and biochemical experiments, we found that cultured cortical neurons treated with the classical BZD, diazepam (DZP), presented no substantial change in surface or synaptic levels of γ2-GABAARs. In contrast, both γ2 and the postsynaptic scaffolding protein gephyrin showed diminished total protein levels following a single DZP treatment in vitro and in mouse cortical tissue. We further identified DZP treatment enhanced phosphorylation of gephyrin Ser270 and increased generation of gephyrin cleavage products. Selective immunoprecipitation of γ2 from cultured neurons revealed enhanced ubiquitination of this subunit following DZP exposure. To assess novel trafficking responses induced by DZP, we employed a γ2 subunit containing an N terminal fluorogen-activating peptide (FAP) and pH-sensitive green fluorescent protein (γ2pHFAP). Live-imaging experiments using γ2pHFAP GABAAR expressing neurons identified enhanced lysosomal targeting of surface GABAARs and increased overall accumulation in vesicular compartments in response to DZP. Using fluorescence resonance energy transfer (FRET) measurements between γ2 and γ2 subunits within a GABAAR in neurons, we identified reductions in synaptic clusters of this subpopulation of surface BZD sensitive receptor. Moreover, we found DZP simultaneously enhanced synaptic exchange of both γ2-GABAARs and gephyrin using fluorescence recovery after photobleaching (FRAP) techniques. Finally we provide the first proteomic analysis of the BZD sensitive GABAAR interactome in DZP vs. vehicle treated mice. Collectively, our results indicate DZP exposure elicits down-regulation of gephyrin scaffolding and BZD sensitive GABAAR synaptic availability via multiple dynamic trafficking processes.
Mapping Structure and Biological Functions within Mesenchymal Bodies using Microfluidics
Authors: Sart Sébastien , Tomasi Raphaël F.-X. , Barizien Antoine , Amselem Gabriel , Cumano Ana , Baroud Charles N.
Published: January 2019

Organoids that recapitulate the functional hallmarks of anatomic structures comprise cell populations able to self-organize cohesively in 3D. However, the rules underlying organoid formationin vitroremain poorly understood because a correlative analysis of individual cell fate and spatial organization has been challenging. Here, we use a novel microfluidics platform to investigate the mechanisms determining the formation of organoids by human mesenchymal stromal cells that recapitulate the early steps of condensation initiating bone repairin vivo. We find that heterogeneous mesenchymal stromal cells self-organize in 3D in a developmentally hierarchical manner. We demonstrate a link between structural organization and local regulation of specific molecular signaling pathways such as NF-κB and actin polymerization, which modulate osteo-endocrine functions. This study emphasizes the importance of resolving spatial heterogeneities within cellular aggregates to link organization and functional properties, enabling a better understanding of the mechanisms controlling organoid formation, relevant to organogenesis and tissue repair.
Comparative analysis of Synthetic Physical Interactions with the yeast centrosome
Authors: Howell Rowan S M , Csikász-Nagy Attila , Thorpe Peter H
Published: January 2019

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The yeast centrosome or Spindle Pole Body (SPB) is situated in the nuclear membrane, where it nucleates spindle microtubules and acts as a signalling hub. Previously, we used Synthetic Physical Interactions to map the regions of the cell that are sensitive to forced relocalization of proteins across the proteome [Berry et al., 2016]. Here, we expand on this work to show that the SPB, in particular, is sensitive to the relocalization of many proteins. This work inspired a new data analysis approach that indicates that relocalization screens may produce more growth defects than previously reported. A set of associations with the SPB result in elevated SPB number and since hyper-proliferation of centrosomes is a hallmark of cancer cells, these associations point the way for the use of yeast models in the study of spindle formation and chromosome segregation in cancer.
How conspicuous are peacock eyespots and other colorful feathers in the eyes of mammalian predators?
Authors: Amador Kane Suzanne , Wang Yuchao , Fang Rui , Lu Yabin , Dakin Roslyn
Published: January 2019

Feathers perceived by humans to be vividly colorful are often presumed to be equally conspicuous to other mammals, and thus to present an enhanced predation risk. However, many mammals that prey on adult birds have dichromatic visual systems with only two types of color-sensitive visual receptors (one sensitive to ultraviolet light), rather than the three characteristic of humans and four of most birds. Thus, understanding how these predators perceive color requires quantitative visual modeling. Here, we use a combination of reflectance spectroscopy, multispectral imaging, color vision modelling and visual texture analysis to compare the visual signals available to conspecifics and to mammalian predators for multicolored feathers from the Indian peacock (Pavo cristatus) as well as red and yellow parrot feathers; we also take into account the effects of distance-dependent blurring due to visual acuity. When viewed by tetrachromatic birds against a background of green vegetation, most of the feathers studied had color and brightness contrasts similar to values previously found for ripe fruit. By contrast, when viewed by dichromat mammalian predators, the color and brightness contrasts of these feathers were only weakly detectable and often did not reach detection thresholds for typical viewing distances. We furthermore show that the peacock’s erect train has undetectable color and brightness contrasts and visual textures when photographed against various foliage backgrounds. Given the similarity of photoreceptor sensitivities and feather reflectance properties across relevant species, these findings are consistent with many feathers of similar hue being inconspicuous, and in some cases potentially cryptic, in the eyes of their mammalian predators. These results suggest that many types of colorful feathers are likely to be cryptic to mammals while providing a communication channel perceptible to birds, while emphasizing the importance of understanding diverse sensory receivers in the evolution of animal coloration.
Dynamics, cariogenicity, and geographic distribution of Streptococcus mutans adhesin types suggest adaptation to individual hosts
Authors: Sheng Nongfei , Esberg Anders , Mårell Lena , Johansson Elisabeth , Källestål Carina , Strömberg Nicklas
Published: January 2019

Dental caries, the most common chronic infectious disease, involve Streptococcus mutans SpaP A/B/C and Cnm/Cbm adhesin types of different virulence. We have explored their stability and dynamics over 5 years, their geographic distribution, as well as the potentially increased cariogenicity of specific SpaP B subtypes. We performed qPCR and TaqMan typing using whole saliva and isolates from 452 Swedish adolescents followed from 12 to 17 years of age. Approximately 50% of the children were infected at baseline with a single dominant (44%) or mixed (6%) SpaP A, B, or C type, some of which were also Cnm (6%) or Cbm (1%) positive. Stability (+, +) was high for S. mutans infection (85%) and dominant SpaP A or C (80% and 67%) and Cnm or Cbm (85% and 100%) types, but low for SpaP B (51%) and mixed SpaP A/B/C types (26%). Only five children switched from one SpaP type to another, and none between Cnm and Cbm types. Mixed SpaP A/B/C types were typically lost or changed into dominant types. Moreover, children infected with Cnm (n=26) types were more frequent in the northern (Skellefteå) region (p = 0.0041), and those with Cbm types (n=7) in the southern (Umeå) region. Children infected with SpaP B-2 subtypes had a doubled caries experience (p = 0.009) and 5-year caries increment (p = 0.02) compared to those infected with SpaP A. In conclusion, the stable dominant but instable mixed adhesin types and geographic differentiation of Cnm and Cbm types suggest adaptation of low and high cariogenicity types to specific individuals.