bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Methylation Levels in CpGs of the BIN1 Gene in Individuals With Alzheimer Disease
Authors: Salcedo-Tacuma David , Melgarejo Jesús D. , Mahecha Maria F. , Ortega-Rojas Jenny , Arboleda-Bustos Carlos E. , Pardo-Turriago Rodrigo , Arboleda Humberto
Published: July 2019

Introduction:

Late-onset Alzheimer disease (LOAD) is the most common dementia worldwide. APOE-ɛ4 and BIN1 (Bridging Integrator 1) have been implicated in the pathogenesis of this disease, but, although DNA methylation of dinucleotide CpGs in the BIN1 gene influences alterations, it has not been studied in Hispanics.

Objective:

The objective of this study was to evaluate the BIN1 3′ intergenic region DNA methylation patterns in a Colombian sample of LOAD patients.

Methods:

A case-control study was conducted in 50 individuals with LOAD and 50 age-sex matched controls to determine associations of LOAD with DNA methylation. DNA was isolated from peripheral blood, and methylation levels of 8 CpGs were estimated by bisulfite conversion followed by Sanger sequencing with direct PCR analysis. Logistic regression models adjusted by age, sex, and APOE were used to calculate risk associations between methylation levels and LOAD.

Results:

Overall, participants with LOAD had significantly lower methylation levels on CpG26 (0.86±0.11 vs. 0.95±0.05; P>0.001), CpG44 (0.84±0.09 vs. 0.94±0.06; P=0.001), and CpG87 (0.64±0.12 vs. 0.82±0.10; P>0.001). Adjusted regression models showed that decreased methylation levels of these CpGs remained as risk factors for LOAD (P<0.05).

Conclusions:

Hypomethylation of CpGs in BIN1 might play an important role in the expression of BIN1 and may be a biomarker for identifying individuals at high risk of developing LOAD.
Neurovascular Dysfunction in Alzheimer Disease
Authors: Cipollini Virginia , Sette Giuliano , Bossù Paola , Ciaramella Antonio , Salani Francesca , De Carolis Antonella , Troili Fernanda , Orzi Francesco , Giubilei Franco
Published: July 2019

Aims:

The aims of this study were to assess vascular dysfunction in patients with Alzheimer disease (AD) by investigating cerebral vasomotor reactivity using transcranial Doppler ultrasound (TCD) and to evaluate any correlations between cerebral vasoreactivity and endothelium dysfunction. Moreover, the frequency of circulating progenitor cells (CPCs) and the blood concentration of vascular/inflammatory markers were evaluated.

Materials and Methods:

We recruited 35 AD subjects and 17 age-matched, sex-matched, and education-matched healthy control subjects. Cerebral vasomotor reactivity was assessed by means of the TCD-based breath-holding index test (BHI). The level of CPCs was evaluated by means of flow cytometry from venous blood samples, while blood vascular/inflammatory markers were measured by means of enzyme-linked immunosorbent assay.

Results:

Both cerebral assay blood flow velocity in the middle cerebral artery (MCAFV) and BHI values were significantly lower in AD subjects than in healthy controls (P<0.05). A positive trend was found between MCAFV and BHI values and Mini-Mental State Evaluation (MMSE) scores. Moreover, the hematopoietic progenitor cells’ count was found to be lower in patients with AD than in controls (P<0.05). Finally, a significantly higher expression of the plasma chemokine CCL-2 was observed in AD patients than in healthy controls.

Conclusions:

Our results confirm that cerebral hemodynamic deterioration may be a critical marker of cognitive decline. Further studies are needed to investigate the role of circulating CPCs and chemokines as potential contributors to neurovascular dysfunction.
Perspectives of African American Older Adults on Brain Health
Authors: Bardach Shoshana H. , Benton Beverly , Walker Charlene , Alfred Doris Love , Ighodaro Eseosa , Caban-Holt Allison , Jicha Gregory A.
Published: July 2019

Background:

Statistics suggest that African Americans have a disproportionately high prevalence of Alzheimer disease (AD), yet are less likely to enroll in AD clinical trials than white individuals. Although research has previously identified various barriers to participation, relatively little is known about how to overcome these barriers and engage African American individuals in AD research. The purpose of this study is to better understand how African Americans conceptualize brain health and their ability to influence healthy brain aging.

Methods:

Three African American community advocates each facilitated a small group of African American participants over 8 to 10 sessions of a photovoice process involving discussion and sharing of images focused on brain health. Sessions were audiotaped and transcribed verbatim and photographs were uploaded.

Findings:

Participants recognized a diversity of what brain health can mean and indicated an interconnectedness between brain health and its influences. Key factors that were identified by group members as key to brain health included lifestyle factors, activity, and engagement and nature, resiliency, and positivity.

Discussion:

These emic insights into perceptions of brain health may represent important foci for targeted messaging strategies to promote brain health and research engagement within the African American population.
Clinical trials in amyotrophic lateral sclerosis
Authors: McDermott Christopher J.
Published: July 2019

Purpose of review

To review new developments in the field of amyotrophic lateral sclerosis (ALS) clinical trial design and to review the implications of the latest ALS clinical trials.

Recent findings

There has been substantial reflection on how clinical trials in ALS are best conducted. The revised Airlie House recommendations are an important milestone and should guide trial design. In addition, innovations using individualized risk-based eligibility criteria, adaptive designs, joint modelling, patient-centred approaches, and remote collection of data show real promise. Edaravone was shown to have benefit on function in a well defined subset of patients with ALS, although there are concerns about the generalizability of the findings. Studies of arimoclomol, inosine, and cellular therapies have demonstrated promising signals in early phase work and are being taken forward into larger studies. Well conducted studies of rasagaline did not show an effect on primary outcome measures.

For many decades there has been regular disappointment with the results of clinical trials. With the innovations in trial design and advances in our basic understanding of the biology of ALS, the prospects for a step change in treatments for people affected by ALS are strong.
Update on amyotrophic lateral sclerosis genetics
Authors: Brenner David , Weishaupt Jochen H.
Published: July 2019

Purpose of review

The fatal motoneuron disease amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder with a high contribution of genetic factors to pathogenesis, in probably both familial and sporadic ALS cases. State-of-the art sequencing techniques continue to reveal novel monogenic causes for ALS, risk factors and modifiers. This leads to an improved genotype/phenotype correlation and is becoming increasingly relevant for genetic diagnosis, counseling and therapy. The first gene-specific therapies are being tested in ongoing clinical trials. Consequently, this review aims to summarize the most important aspects of ALS genetics of the past 2 years.

Recent findings

Most recent disease gene discoveries in the field of ALS constitute the genes KIF5A, ANXA11, GLT8D1 and TIA1, as well as an array of novel risk factors and modifiers. Increasing evidence suggests that even ALS mutations with high penetrance can co-occur with additional mutations in other known ALS genes, suggesting a relevant role of digenetic or polygenetic modes of inheritance. Genotype/phenotype correlation reveals clinical pleiotropy for several ALS genes, which can be linked, for example, to ataxia or Parkinsonian syndromes beyond classical ALS and frontotemporal dementia (FTD) phenotypes.

The field of ALS continues to develop rapidly with multiple disease gene discoveries per year. The relevance of these findings for genetic counseling and diagnosis is obvious. With gene-specific therapies being tested in a clinical setting, the relevance of genetic aspects of ALS is increasing and likely to be linked to therapeutic consequences in the near future.
Time Is Brain: The Use of EEG Electrode Caps to Rapidly Diagnose Nonconvulsive Status Epilepticus
Authors: McKay Jake H. , Feyissa Anteneh M. , Sener Ugur , D'Souza Caitlin , Smelick Chris , Spaulding Aaron , Yelvington Kirsten , Tatum William O.
Published: July 2019

Objective:

To perform a feasibility pilot study comparing the usefulness of EEG electrode cap versus standard scalp EEG for acquiring emergent EEGs in emergency department, inpatient, and intensive care unit patients.

Background:

Nonconvulsive status epilepticus (NCSE) is a neurological emergency diagnosed exclusively by EEG. Nonconvulsive status epilepticus becomes more resistant to treatment 1 hour after continued seizure activity. EEG technologists are alerted “stat” when there is immediate need for an EEG during oncall hours, yet delays are inevitable. Alternatively, EEG caps can be quickly placed by in-house residents at bedside for assessment.

Design/Methods:

EEG caps were compared with standard-of-care “stat” EEGs for 20 patients with suspected NCSE. After the order for a stat EEG was placed, neurology residents were simultaneously alerted and placed an EEG cap prior to the arrival of the on-call out-of-hospital technologist. Both EEG cap recordings and standard EEG recordings were visually reviewed at 10 and 20 minutes in a blinded manner by two electroencephalographers. The timing, accuracy of interpretation, and diagnosis between the two techniques were then compared.

Results:

Of the 20 adult patients, 70% (14 of 20) of EEG cap recordings were interpretable, whereas 95% (19 of 20) standard EEGs were interpretable; three had findings consistent with NCSE on both the EEG cap and standard EEG recordings. In the time analysis, 16 patients were included. EEG cap placement was significantly more time efficient than an EEG performed by technologist using the usual “stat” EEG protocol, with the median EEG cap electrode placement occurring 86 minutes faster than standard EEG (22.5 minutes vs. 104.5 minutes; P < 0.0001; n = 16).

Conclusions:

New rapid EEG recording using improved EEG caps may allow for rapid diagnosis and clinical decision making in suspected NCSE.
Automated Processing of Single-Channel Surface Electromyography From Generalized Tonic–Clonic Seizures to Inform Semiology
Authors: Cardenas Damon P. , Halford Jonathan J. , Whitmire Luke E. , Morgan Lola C. , Lie Octavian V. , Jetter Gina M. , Cavazos Jose E.
Published: July 2019

Purpose:

Advances in surface electromyography (sEMG) monitoring allow for long-term data collection in a natural environment, giving objective information that may identify risk of sudden unexpected death in epilepsy and guide clinical decision-making. Generalized tonic–clonic seizure semiology, namely motor tonic and clonic phase duration, may be an important factor in determining the level of seizure control and risk of sudden unexpected death in epilepsy. This study demonstrates a quantitative analysis of sEMG collected with a dedicated wearable device.

Methods:

During routine monitoring, 23 generalized tonic–clonic seizures from 19 subjects were simultaneously recorded with video-EEG and sEMG. A continuous wavelet-transform was used to determine the frequency components of sEMG recorded during generalized tonic–clonic seizures. An automated process, incorporating a variant of cross-validation, was created to identify ideal frequencies and magnitude ranges for tonic and clonic phases and determine phase durations. Phase durations determined using sEMG analysis were compared with phase durations determined by independent epileptologists' review of video-EEG.

Results:

Cross-validation revealed that the optimal frequency bands for tonic and clonic phases are 150 to 270 Hz and 12 to 70 Hz, respectively. The average difference in phase duration calculated using the two methods for tonic and clonic phases and total seizure duration were −0.42 ± 4.94, −5.12 ± 9.68, and −5.11 ± 11.33 seconds, respectively (results presented are TsEMG − TvEEG, μ ± σ).

Conclusions:

The automated processing of sEMG presented here accurately identified durations of tonic, clonic, and total motor durations of generalized tonic–clonic seizures similar to durations identified by epileptologists' review of video-EEG.
Appliance of Navigated Transcranial Magnetic Stimulation in Radiosurgery for Brain Metastases
Authors: Tokarev Alexey S. , Rak Viacheslav A. , Sinkin Mikhail V. , Evdokimova Olga L. , Stepanov Valentin N. , Koynash Greg V. , Krieg Sandro M. , Krylov Vladimir V.
Published: July 2019

Purpose:

Navigated transcranial magnetic stimulation (nTMS) provides noninvasive visualization of eloquent brain areas. The nTMS is usually applied in presurgical planning to minimize the risk of surgery-related neurological deterioration. The aim of this study was to evaluate the usefulness of nTMS data for GammaKnife treatment planning for patients suffering from brain metastases.

Methods:

Motor cortex mapping with nTMS was performed in eight patients with brain metastases within or adjacent to the precentral gyrus. The nTMS data set was imported into the planning software and fused with anatomical MRI. Then contouring of the target and critical structures was performed. Treatment plans with and without visualization of the functional structures by nTMS were analyzed and compared by neurosurgeon and medical physicist.

Results:

The primary motor cortex was successfully delineated even in all cases despite significant peritumoral edema. Beam shaping and combined isocenters were used for conformal dose distribution and steeper dose fall-off near the identified eloquent zone. Compared with plans without nTMS data, treatment plans with integration of cortical nTMS mapping data showed a 2% to 78% (mean, 35.2% ± 22.7%) lower 12-Gy volume within the motor cortex without reduction of the dose applied to the tumor.

Conclusions:

The presented approach allows the easy and reliable integration of neurophysiological mapping data into GammaKnife treatment plans by the standard GammaPlan software. Diminishing the dose to critical structures might help to minimize side effects and therefore improve quality of life for brain metastasis patients.
Effect of training on evidence-based practice to undergraduate dental students: pre and postexperimental study
Authors: Wadgave Umesh , Khairnar Mahesh R. , Kadu Tanvi S. , Chadha Gagandeep K. , Wadgave Yogesh
Published: July 2019

Background:

Evidence-based practice (EBP) training is essential for undergraduate students in making sound clinical decisions during patient care. However, EBP training is not included in the curriculum of undergraduate dental students in India and there is a dearth of research that assessed the effectiveness of EBP training in India. Hence, this study aimed to assess the effectiveness of EBP training to dental undergraduate students.

Methods:

Final year undergraduate students and interns of a dental institution participated in this pre and postexperimental study. All the participants received a 2-day workshop (didactic lectures, hands-on and group activities) in a classroom setting. A validated 35 item instrument titled EBP Knowledge, Attitudes, Access and Confidence questionnaire was used for the outcome assessment of EBP training.

Results:

Fifty undergraduate students (33 interns and 17 final year) participated in the study. Statistically significant improvement was observed in six out of 10 items related to EBP knowledge. All the items related to attitude showed a significant positive change in scores. Only four out of nine items related to accessing evidence showed a statistically significant change. Participants reported moderate confidence gain in critical appraisal skills.

Conclusion:

The current study demonstrated moderate improvement in the effectiveness of EBP training in improving EBP knowledge, accessing evidence and critical appraisal skills.
At the invasion front, male cane toads (Rhinella marina) have smaller testes
Authors: Friesen Christopher R. , Shine Richard
Published: July 2019

As a colonizing species expands its range, individuals at the invasion front experience different evolutionary pressures than do those at the range-core. For example, low densities at the edge of the range mean that males should rarely experience intense sperm competition from rivals; and investment into reproduction may trade-off with adaptations for more rapid dispersal. Both of these processes are predicted to favour a reduction in testis size at the invasion front. To explore effects of invasion stage in Australian cane toads (Rhinella marina), we collected and dissected 214 adult males from three regions: one in the species' range-core (northeastern Australia), and two from invasion fronts (one in northwestern Australia and one in southeastern Australia). Despite the brief duration of separation between toads in these areas (approx. 85 years), testis masses averaged greater than 30% higher (as a proportion of body mass) in range-core males than in conspecifics sampled from either vanguard of the invasion. Previous work has documented low reproductive frequencies in female cane toads at the invasion front also, consistent with the hypothesis that evolutionary and ecological pressures unleashed by an invasion can favour relatively low resource allocation to reproduction in both sexes.
RETRACTED: Involvement of miR-4262 in paclitaxel resistance through the regulation of PTEN in non-small cell lung cancer
Authors: Sun Hongwen , Zhou Xiaoting , Bao Yanan , Xiong Guosheng , Cui Yue , Zhou Hua
Published: July 2019

Non-small cell lung cancer (NSCLC) is considered to be the primary cause of cancer-related mortalities worldwide. Paclitaxel (PTX), either as a monotherapy or in combination with other drugs, is an alternative therapy for advanced NSCLC. However, cancer cell resistance against PTX represents a major clinical problem. This study aimed to investigate the role and underlying mechanism of miR-4262 in PTX-resistant NSCLC. The levels of miR-4262 were analysed by quantitative reverse transcription polymerase chain reaction. A luciferase reporter assay and bioinformatics were used to explore the potential target gene of miR-4262. Regulation of miR-4262 and PTEN expressions in NSCLC was conducted by transfection. PTX-resistant A549 and H1299 cells were established by stepwise screening through increasing the PTX concentration in the cultures.
In vivo
, tumorigenesis experiments were used to explore the effects of miR-4262 and PTX. Cell proliferation, apoptosis and cell migration were detected using a CCK-8 assay, flow cytometry and Transwell migration assay, respectively. PI3 K/Akt pathway-related proteins were detected by western blot. miR-4262 expression was significantly upregulated in NSCLC tissues and cell lines, and miR-4262 targeted PTEN. In addition, miR-4262 induced PTX chemoresistance by promoting survival and migration in A549/PTX and H1299/PTX cells. Moreover, miR-4262 expression and PI3 K/Akt signalling pathway-related proteins were upregulated and PTEN was downregulated in A549/PTX and H1299/PTX. Our results indicate that miR-4262 enhances PTX resistance in NSCLC cells through targeting PTEN and activating the PI3 K/Akt signalling pathway. The inhibition of miR-4262 expression might be an improved treatment to overcome PTX resistance in NSCLC.
Differential expression of selected microRNA and putative target genes in peripheral blood cells as early markers of severe forms of dengue
Authors: Hapugaswatta Harsha , Amarasena Pubudu , Premaratna Ranjan , Seneviratne Kapila N. , Jayathilaka Nimanthi
Published: July 2019

Background

Dengue presents a wide clinical spectrum including asymptomatic dengue fever (DF) or severe forms, such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Early symptoms of DHF are similar to those of non-life-threatening DF. Severe symptoms manifest after 3-5 days of fever, which can be life threatening due to lack of proper medications and inability to distinguish severe cases during the early stages. Early prediction of severe dengue in patients with no warning signs who may later develop severe infection is very important for proper disease management to alleviate DHF related complications and mortality. Due to the role in post-transcriptional regulation of gene expression and remarkable stability of microRNA, altered expression of microRNA was evaluated to explore clinically relevant biomarkers.

Methodology/Principal findings

The relative expression of microRNA hsa-let-7e, hsa-miR-30b-5p, hsa-miR-30e-3p, hsa-miR-33a, and hsa-miR-150-5p and several putative target genes in peripheral blood cells (PBC) collected from 20 DF and 20 DHF positive patients within four days from fever onset was evaluated by qRT-PCR. hsa-miR-150-5p showed significant (P<0.05) up regulation in PBC of DHF patients compared to DF patients during the acute phase of infection. Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P<0.05) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in DHF patients during the early stage of infection.

Conclusions/Significance

Differential expression of microRNA miR-150-5p and the putative target gene EZH2 may serve as reliable biomarkers of disease severity during early stages of dengue infection.

Author summary

Severe dengue cannot be distinguished from dengue fever during the early stages of infection based on the clinical symptoms. A diagnosis is only made after the patient is presented with severe manifestations such as plasma leakage and hemorrhage. During a dengue outbreak, this leads to high occupancy of hospital beds. However, only a small percentage of patients present with severe symptoms and the others do not require medical care at a hospital. Therefore, early prognosis of severe manifestations could reduce dengue related mortality by identifying the patients who will benefit from hospitalization and early intervention. We demonstrate that severe dengue in Sri Lankan patients is associated with increased expression of miRNA miR150 and decreased expression of EZH2 during the early stages of infection when none of the patients showed symptoms of developing severe manifestations at later stages of infection.
A pooled analysis of the duration of chemoprophylaxis against malaria after treatment with artesunate-amodiaquine and artemether-lumefantrine
Authors: Bretscher MT , Dahal P , Griffin J , Stepniewska K , Bassat Q , Baudin E , D’Alessandro U , Djimde AA , Dorsey G , Espié E , Fofana B , González R , Juma E , Karema C , Lasry E , Lell B , Lima N , Menéndez C , Mombo-Ngoma G , Moreira C , Nikiema F , Ouédraogo JB , Staedke SG , Tinto H , Valea I , Yeka A , Ghani AC , Guerin PJ , Okell LC
Published: July 2019

Artemether-lumefantrine (AL) and artesunate-amodiaquine (AS-AQ) are the most commonly-used treatments against Plasmodium falciparum malaria in Africa. The lumefantrine and amodiaquine partner drugs may provide differing durations of post-treatment prophylaxis, an important additional benefit to patients. Analyzing 4214 individuals from clinical trials in 12 sites, we estimated a mean duration of post-treatment protection of 13.0 days (95% CI 10.7-15.7) for AL and 15.2 days (95% CI 12.8-18.4) for AS-AQ after allowing for transmission intensity. However, the duration varied substantially between sites: where wild type pfmdr1 86 and pfcrt 76 parasite genotypes predominated, AS-AQ provided ∼2-fold longer protection than AL. Conversely, AL provided up to 1.5-fold longer protection than AS-AQ where mutants were common. We estimate that choosing AL or AS-AQ as first-line treatment according to local drug sensitivity could alter population-level clinical incidence of malaria by up to 14% in under-five year olds where malaria transmission is high.
Analysis of common and rare VPS13C variants in late onset Parkinson disease
Authors: Rudakou Uladzislau , Ruskey Jennifer A. , Krohn Lynne , Laurent Sandra B. , Spiegelman Dan , Greenbaum Lior , Yahalom Gilad , Desautels Alex , Montplaisir Jacques Y. , Fahn Stanley , Waters Cheryl H. , Levy Oren , Kehoe Caitlin M. , Narayan Sushma , Dauvilliers Yves , Dupré Nicolas , Hassin-Baer Sharon , Alcalay Roy N. , Rouleau Guy A. , Fon Edward A. , Gan-Or Ziv
Published: July 2019

Objective

We aimed to study the role of coding VPS13C variants in a large cohort of late-onset PD (LOPD) patients.

Methods

VPS13C and its untranslated regions were sequenced using targeted next-generation sequencing in 1,567 PD patients and 1,667 controls from 3 cohorts. Association tests of rare potential homozygous and compound heterozygous variants and burden tests for rare heterozygous variants were performed. Common variants were analyzed using logistic regression adjusted for age and sex in each of the cohorts, followed by a meta-analysis.

Results

No bi-allelic carriers of rare VPS13C variants were found among patients and two carriers of compound heterozygous variants were found in two controls. There was no statistically significant burden of rare (MAF<1%) or very rare (MAF<0.1%) coding VPS13C variants in PD. A VPS13C haplotype including the p.R153H-p.I398I-p.I1132V-p.Q2376Q variants was nominally associated with a reduced risk for PD (meta-analysis of the tagging SNP p.I1132V (OR=0.48, 95%CI=0.28-0.82, p=0.0052). This haplotype was not in linkage disequilibrium (LD) with the known genome-wide association study (GWAS) top hit.

Conclusions

Our results do not support a role for rare heterozygous or bi-allelic VPS13C variants in LOPD. Additional genetic replication and functional studies are needed to examine the role of the haplotype identified here associated with reduced risk for PD.
Minor deviations from randomness have huge repercussions on the functional structuring of sequence space
Authors: Weidmann Laura , Dijkstra Tjeerd , Kohlbacher Oliver , Lupas Andrei N.
Published: July 2019

Approaches based on molecular evolution have organized natural proteins into a hierarchy of families, superfamilies, and folds, which are often pictured as islands in a great sea of unrealized and generally non-functional polypeptides. In contrast, approaches based on information theory have substantiated a mostly random scatter of natural proteins in global sequence space. We evaluate these opposing views by analyzing fragments of a given length derived from either a natural dataset or different random models. For this, we compile distances in sequence space between fragments within each dataset and compare the resulting distance distributions between sets. Even for 100-mers, more than 95% of distances can be accounted for by a random sequence model that incorporates the natural amino acid frequency of proteins. When further accounting for the specific residue composition of the respective fragments, which would include biophysical constraints of protein folding, more than 99% of all distances can be modeled. Thus, while the local space surrounding a protein is almost entirely shaped by common descent, the global distribution of proteins in sequence space is close to random, only constrained by divergent evolution through the requirement that all intermediates connecting two forms in evolution must be functional.

Significance Statement

When generating new proteins by evolution or design, can the entire sequence space be used, or do viable sequences mainly occur only in some areas of this space? As a result of divergent evolution, natural proteins mostly form families that occupy local areas of sequence space, suggesting the latter. Theoretical work however indicates that these local areas are highly diffuse and do not dramatically affect the statistics of sequence distribution, such that natural proteins can be considered to effectively cover global space randomly, though extremely sparsely. By comparing the distance distribution of natural sequences to that of various random models, we find that they are indeed distributed largely randomly, provided that the amino acid composition of natural proteins is respected.
Live cell kinetic analysis of the LMO2/LDB1 leukemogenic protein complex reveals a hierarchy of turnover with implications for complex assembly
Authors: Layer Justin H. , Christy Michael , Placek Lindsay , Unutmaz Derya , Guo Yan , Davé Utpal P.
Published: July 2019

Multisubunit protein complexes operate in many cellular functions. The LDB1/LMO2 macromolecular complex has been posited to be critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as bHLH and GATA transcription factors. We analyzed the steady state abundance and kinetic stability of LMO2 and its partners via HALO protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stability, with half lives in descending order: LDB1>SSBP>LMO2>TAL1. Importantly, LDB1 conferred enhanced stability upon each and every subunit component and nucleated the formation of the multisubunit protein complex. Our studies provide significant insights into LDB1/LMO2 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.
Why we publish where we do: Faculty publishing values and their relationship to review, promotion and tenure expectations
Authors: Niles Meredith T. , Schimanski Lesley A. , McKiernan Erin C. , Alperin Juan P.
Published: July 2019

Using an online survey of academics at 55 randomly selected institutions across the US and Canada, we explore priorities for publishing decisions and their perceived importance within review, promotion, and tenure (RPT). We find that respondents most value journal readership, while they believe their peers most value prestige and related metrics such as impact factor when submitting their work for publication. Respondents indicated that total number of publications, number of publications per year, and journal name recognition were the most valued factors in RPT. Older and tenured respondents (most likely to serve on RPT committees) were less likely to value journal prestige and metrics for publishing, while untenured respondents were more likely to value these factors. These results suggest disconnects between what academics value versus what they think their peers value, and between the importance of journal prestige and metrics for tenured versus untenured faculty in publishing and RPT perceptions.
Transposable elements have contributed human regulatory regions that are activated upon bacterial infection
Authors: Bogdan Lucia , Barreiro Luis , Bourque Guillaume
Published: July 2019

Transposable elements (TEs) are increasingly recognized as important contributors to mammalian regulatory systems. For instance, they have been shown to play a role in the human interferon response. However, their involvement in other mechanisms of immune cell activation remains poorly understood. We investigated the profile of accessible chromatin enhanced in stimulated human macrophages using ATAC-Seq to assess the role of different TE subfamilies in regulating the immune response. We found that both previously identified and new repeats belonging to the MER44, THE1, Tigger3 and MLT1 families provide 14 subfamilies that are enriched in differentially accessible chromatin and found near differentially expressed genes. These TEs also harbour binding motifs for several candidate transcription factors, including important immune regulators AP-1 and NF-kB, present in 96% of accessible MER44B and 83% of THE1C instances, respectively. To more directly assess their regulatory potential, we evaluated their presence in regions putatively affecting gene expression, as defined by quantitative trait locus (QTL) analysis, and find that repeats are also contributing to accessible elements near QTLs. Together, these results suggest that a number of TE families have contributed to the regulation of the immunogenomic response to infection in humans.
Vascular Expression of Hemoglobin Alpha in Antarctic Icefish Supports Iron Limitation as Novel Evolutionary Driver
Authors: Corliss Bruce A. , Delalio Leon J. , Keller T.C. Stevenson , Keller Alexander S. , Keller Douglas A. , Corliss Bruce H. , Bjork Adam C , Beers Jody M. , Peirce Shayn M. , Isakson Brant E.
Published: July 2019

Frigid temperatures of the Southern Ocean are known to be an evolutionary driver in Antarctic fish. For example, many fish have reduced red blood cell (RBC) concentration to minimize vascular resistance. Via the oxygen-carrying protein hemoglobin, RBCs contain the vast majority of the body’s iron, which is known to be a limiting nutrient in marine ecosystems. Since lower RBC levels also lead to reduced iron requirements, we hypothesized that low iron availability was an additional evolutionary driver of Antarctic fish speciation. Antarctic Icefish of the familyChannichthyidaeare known to have extreme alteration of iron metabolism due to loss of two iron-binding proteins, hemoglobin and myoglobin, and no RBCs. Loss of hemoglobin is considered a maladaptive trait allowed by relaxation of predator selection, since extreme adaptations are required to compensate for the loss of oxygen-carrying capacity. However, iron dependency minimization may have driven hemoglobin loss instead of a random evolutionary event. Given the variety of functions that hemoglobin serves in the endothelium, we suspected the protein corresponding to the 3’ truncated Hbα fragment (Hbα-3’f) that was not genetically excluded by icefish, may still be expressed as a protein. Using whole mount confocal microscopy, we show that Hbα-3’f is expressed in the vascular endothelium of icefish retina, suggesting this Hbα fragment may still serve an important role in the endothelium. These observations support a novel hypothesis that iron minimization could have influenced icefish speciation with the loss of the iron-binding portion of Hbα in Hbα-3’f, as well as hemoglobin β and myoglobin.
Apple ripening is controlled by a NAC transcription factor
Authors: Migicovsky Zoë , Yeats Trevor H. , Watts Sophie , Song Jun , Forney Charles F. , Burgher-MacLellan Karen , Somers Daryl J. , Gong Yihi , Zhang Zhaoqi , Vrebalov Julia , Giovannoni James G. , Rose Jocelyn K. C. , Myles Sean
Published: July 2019

Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of ripening and associated textural changes are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene,NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ∼800 apple accessions. In this population, we compared a genetic marker withinNAC18.1to markers targeting three other firmness-related genes currently used by breeders (ACS1,ACO1, andPG1), and found that theNAC18.1marker was the strongest predictor of both firmness at harvest and firmness after three months of cold storage. By sequencingNAC18.1across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences.NAC18.1encodes a protein with high similarity to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). To test whether these genes are functionally orthologous, we introduced bothNAC18.1transgene haplotypes into the tomatonormutant and showed that both haplotypes complement thenorripening deficiency. Taken together, these results indicate that polymorphisms inNAC18.1may underlie substantial variation in apple firmness through modulation of a conserved ripening program.
Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence
Authors: Goodheart Jessica A. , Minsky Geetanjali , Brynjegard-Bialik Mira N. , Drummond Michael S. , Munoz J. David , Fallon Timothy R. , Schultz Darrin T. , Weng Jing-Ke , Torres Elizabeth , Oakley Todd H.
Published: July 2019

Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination of the biosynthethic pathways of the luciferins. Other groups, including terrestrial fireflies, do synthesize their own luciferin, but culturing them is difficult, and the biosynthetic pathway for firefly luciferin remains unclear. An additional independent origin of endogenous bioluminescence is found within ostracods from the family Cypridinidae, which use their luminescence for defense and, in Caribbean species, for courtship displays. Here, we report the first complete life cycle of a luminous ostracod (Vargula tsujii Kornicker & Baker, 1977, the California Sea Firefly) in the laboratory. We also describe the late-stage embryogenesis of Vargula tsujii and discuss the size classes of instar development. We find embryogenesis in V. tsujii ranges from 25-38 days, and this species appears to have five instar stages, consistent with ontogeny in other cypridinid lineages. We estimate a complete life cycle at 3-4 months. We also present the first complete mitochondrial genome for Vargula tsujii. Bringing a luminous ostracod into laboratory culture sets the stage for many potential avenues of study, including learning the biosynthetic pathway of cypridinid luciferin and genomic manipulation of an autogenic bioluminescent system.
Describing the fecal metabolome in cryogenically collected samples from healthy participants
Authors: Trošt Kajetan , Ahonen Linda , Suvitaival Tommi , Christiansen Nina , Nielsen Trine , Thiele Maja , Jacobsen Suganya , Krag Aleksander , Rossing Peter , Hansen Torben , Dragsted Lars Ove , Legido-Quigley Cristina
Published: July 2019

Introduction

The chemical composition of feces plays an important role in human metabolism. Metabolomics and lipidomics are valuable tools for screening the metabolite composition in feces. Here we set out to describe fecal metabolite composition in healthy participants in frozen stools.

Methods

Frozen stool samples were collected from 10 healthy volunteers and cryogenically drilled in four areas along the specimen. Polar metabolites were analyzed using derivatization followed by two-dimensional gas chromatography and time of flight mass spectrometry. Lipids were detected using ultra high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry. The technical variation threshold was set to 30% in pooled quality control samples and metabolite variation was then assessed in four areas per specimen. A data-generated network using metabolites found in all areas was computed for healthy participants.

Results

2326 metabolic features were detected. Out of a total of 298 metabolites that were annotated we report here 185 that showed a technical variation of x< 30%. These metabolites included amino acids, fatty acid derivatives, carboxylic acids and phenolic compounds. Lipids predominantly belonged to the groups of diacylglycerols, triacylglycerols and ceramides. Metabolites varied between sampling areas (14%-80%). A network using metabolites present in all areas showed two main clusters, DAG lipids and phenyllactic acid.

Conclusions

In feces from healthy participants, the main groups detected were phenolic compounds, ceramides, diacylglycerols and triacylglycerols. Metabolite levels differed considerably depending on the sampling area.
Graphing and reporting heterogeneous treatment effects through reference classes
Authors: Watson James A. , Holmes Chris C.
Published: July 2019

Background

Exploration and modelling of individual treatment effects and treatment heterogeneity is an important aspect of precision medicine in randomized controlled trials (RCTs). The usual approach is to develop a predictive model for individual outcomes and then look for an interaction effect between treatment allocation and important patient covariates. However, such models are prone to overfitting and multiple testing, and typically demand a transformation of the outcome measurement, for example, from the absolute risk in the original RCT to log-odds of risk in the predictive model.

Methods

We show how reference classes derived from background information can be used to alleviate this problem through a two-stage approach where we first estimate a key aspect of heterogeneity in the trial population and then explore for an interaction with the treatment effect along this axis of variation. This bypasses the search for interactions, protecting against multiple testing, and allows for exploration of heterogeneous treatment effects on the original outcome scale of the RCT. This would typically be applied to multivariate models of baseline risk to assess the stability of average treatment effects with respect to the distribution of risk in the population studied. We show how ‘local’ and ‘tilting’ schemes based on ranking patients by baseline risk can be used as a general approach for exploring heterogeneity of treatment effect.

Results

We illustrate this approach using the single largest randomised treatment trial in severe falciparum malaria and show how the estimated treatment effect in terms of absolute mortality risk reduction increases considerably for higher risk strata.
Heterogeneity in Nucleosome Spacing Governs Chromatin Elasticity
Authors: Beltran Bruno , Kannan Deepti , MacPherson Quinn , Spakowitz Andrew J.
Published: July 2019

Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain (WLC) model to include statistically spaced, rigid kinks. On time scales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can differ by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer time scales, we show that continuous re-randomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that heterogeneity in nucleosome spacing acts as the dominant source of chromatin elasticity and governs both local and global chromatin organization.
Biases in GWAS – the dog that did not bark
Authors: Schooling C M
Published: July 2019

Background

Genome wide association studies (GWAS) of specific diseases are central to scientific discovery. Bias from inevitably recruiting only survivors of genetic make-up and disease specific competing risk has not been comprehensively considered.

Methods

We identified sources of bias using directed acyclic graphs, and tested for them in the UK Biobank GWAS by making comparisons across the survival distribution, proxied by age at recruitment.

Results

Associations of genetic variants with some diseases depended on their effect on survival. Variants associated with common harmful diseases had weaker or reversed associations with subsequent diseases that shared causes.

Conclusion

Genetic studies of diseases that involve surviving other common diseases are open to selection bias that can generate systematic type 2 error. GWAS ignoring such selection bias are most suitable for monogenetic diseases. Genetic effects on age at recruitment may indicate potential bias in disease-specific GWAS and relevance to population health.
PEMA: from the raw .fastq files of 16S rRNA and COI marker genes to the (M)OTU-table, a thorough metabarcoding analysis
Authors: Zafeiropoulos Haris , Viet Ha Quoc , Vasileiadou Katerina , Potirakis Antonis , Arvanitidis Christos , Topalis Pantelis , Pavloudi Christina , Pafilis Evangelos
Published: July 2019

Background

Environmental DNA (eDNA) and metabarcoding, allow the identification of a mixture of individuals and launch a new era in bio- and eco-assessment. A number of steps are required to obtain taxonomically assigned (Molecular) Operational Taxonomic Unit ((M)OTU) tables from raw data. For most of these, a plethora of tools is available; each tool’s execution parameters need to be tailored to reflect each experiment’s idiosyncrasy. Adding to this complexity, for such analyses, the computation capacity of High Performance Computing (HPC) systems is frequently required.

Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise are programming languages specialized for big data pipelines, incorporating features like roll-back checkpoints and on-demand partial pipeline execution.

Findings

PEMA is a containerized assembly of key metabarcoding analysis tools with a low effort in setting up, running and customizing to researchers’ needs. Based on third party tools, PEMA performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Due to its simplified parameterisation and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against previously published datasets and achieved comparable quality results.

Conclusions

Given its time-efficient performance and its quality results, it is suggested that PEMA can be used for accurate eDNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.