bluuebunny/crossref_metadata_2025 huggingface dataset:
Fumarase-deficient Uterine Leiomyomas
Authors: Miettinen Markku , Felisiak-Golabek Anna , Wasag Bartosz , Chmara Magdalena , Wang Zengfeng , Butzow Ralf , Lasota Jerzy
Published: July 2016

Loss-of-function germline mutations in the fumarase (FH) gene of the Krebs cycle characterize hereditary leiomyomatosis and renal cell cancer syndrome. Fumarase (FH) deficiency can be diagnosed by the loss of immunohistochemical expression. In this study, we investigated the occurrence and clinicopathologic features of FH-deficient uterine smooth muscle tumors (SMTs). A total of 1583 uterine and 157 nonuterine SMTs were examined using a polyclonal FH antibody and automated immunohistochemistry, and 86 uterine leiomyomas with an FH loss were identified. The frequencies of FH deficiency for subcohorts of uterine SMTs were 1.6% for unselected nonatypical leiomyomas, 1.8% for cellular leiomyomas, 37.3% for atypical leiomyomas, and 0% for leiomyosarcomas. One extrauterine, retroperitoneal estrogen receptor–positive leiomyoma was also FH deficient. The patient age of FH-deficient uterine leiomyomas was 20 to 52 years (median, 38 y). Grossly, these tumors were often soft and amorphous resembling a fibrothecoma. Histologically, the FH-deficient nonatypical leiomyomas lacked cellular packeting and distinct collagenous zones and showed chain-like or palisading nuclear arrangements, prominent staghorn-shaped blood vessels, oval nuclei with no or at most mild atypia, small eosinophilic nucleoli, and a low mitotic rate (0 to 1/10 HPF). The FH-deficient atypical leiomyomas had nuclear atypia often manifesting as multinucleation, prominent eosinophilic nucleoli, and mitotic activity up to 7/10 HPF, with atypical mitoses seen in 32% of cases. However, similar histologic changes were seen in some non–FH-deficient atypical leiomyomas. Loss-of-function FH-gene mutations including 5 whole-gene deletions and 3 frameshift mutations were identified in 8 of 16 FH-deficient nonatypical leiomyomas using multiplex ligation-dependent probe amplification and Sanger sequencing, respectively. Follow-up data on patients with FH-deficient atypical uterine leiomyomas revealed 19 patients alive (median follow-up 27 y) and 5 patients dead. Deaths occurred 9 to 30 years after surgery at a median age of 72 years; causes of death could not be determined. These results indicate that FH-deficient uterine leiomyomas occur with a high frequency among atypical leiomyomas and infrequently in nonatypical leiomyomas and are often histologically distinctive. They seem to have a low biological potential and lack any significant association with leiomyosarcoma.
“Dissecting Gonadoblastoma” of Scully
Authors: Kao Chia-Sui , Idrees Muhammad T. , Young Robert H. , Ulbright Thomas M.
Published: July 2016

Dr Robert E. Scully, who recognized and defined gonadoblastoma (GB), used the term “dissecting gonadoblastoma” (DGB) to describe variants with either an infiltrative type or diffuse pattern instead of the usual small nested arrangement. These patterns have not been emphasized in the literature. To investigate the features of DGB we examined 50 GBs microscopically and performed immunohistochemistry (IHC) in some. DGB was found in 38 (76%) GBs and was represented by 3 patterns. The most frequent was solid/expansile (n=26), consisting of large coalescent nests of germ cells, often (92%) interrupted by fibrovascular septa, with usually minor numbers of sex cord cells. Less frequent were small anastomosing nests (n=24) and cord-like arrangements (n=22) of germ cells irregularly distributed in a prominent stroma and with mostly inconspicuous sex cord cells. Most DGBs (24) showed >1 pattern and demonstrated the characteristic globular deposits of basement membrane, although these were often subtle. The germ cells in all patterns varied from spermatogonium-like to seminoma-like; OCT3/4 was positive only in the latter (7/7). The sex cord cells were small with dense, oval or angulated nuclei, inconspicuous nucleoli, and positivity for inhibin (9/9, strong), FOXL2 (9/9, strong), SF1 (8/9, strong), SOX9 (9/9, weak and focal), WT1 (5/7, variable), and calretinin (3/7, variable). Granulomas were present in 84% of germinoma foci, 13% of DGB foci, and 8% of classic GB foci. Twenty two of 38 DGBs had associated germinoma; 3 also had embryonal carcinoma, yolk sac tumor, and choriocarcinoma, respectively. Follow-up of 2 cases lacking an invasive tumor showed that both patients were disease free at 13 and 4.8 years after bilateral gonadectomy. We conclude that DGB is commonly seen with classic GB and displays identical IHC features, supporting it as a morphologic variant of GB. It appears likely that cord-like DGB is the earliest phase in a GB developmental continuum that may proceed successively into anastomosing, nested (classic GB), and solid/expansile patterns. DGB often mimics germinoma because of the large size of the nests, pseudoinfiltrative pattern of some cases, and inconspicuous sex cord cells. The presence of sex cord cells (identification aided by IHC for sex cord markers), the heterogenous morphology of the germ cells, and globules of basement membrane are useful differential features. The lack of a granulomatous reaction also favors DGB over germinoma. Mistaking DGB for GB with invasive germinoma may result in more aggressive therapy than warranted. The likely relationship of DGB to the relatively recently described concept of so-called “undifferentiated gonadal tissue” is discussed herein.
Clonidine Overdose in a Toddler Due to Accidental Ingestion of a Compounding Cream
Authors: Cates Alexis L. , Wheatley Scott M. , Katz Kenneth D.
Published: July 2016

A 22-month-old girl without any significant medical history accidentally consumed a small amount of a therapeutic compounding cream that contained camphor, gabapentin, clonidine, ketoprofen, and lidocaine. Upon presentation to the emergency department, the child exhibited immediate onset of altered mental status with wide fluctuation in her vital signs, which included intermittent apnea requiring bag-valve mask assistance and endotracheal intubation. Serum laboratory analysis measured a clonidine level of 2.6 ng/mL and undetectable camphor, gabapentin, and ketoprofen levels. While on mechanical ventilation, the patient exhibited hypothermia, bradycardia, and hypotension; all of which responded to supportive care. After approximately 12 hours in the intensive care unit, the patient was successfully extubated and remained asymptomatic. This unique case of a patient with brief, unintentional oral exposure to a compounding cream, who demonstrated severe toxicity despite only a measured, supratherapeutic clonidine concentration, is discussed. Emergency physicians and pediatricians should be alert to the potential for exposure of pediatric patients to these medicinal compounds. Furthermore, parents must be made aware of the potential dangers of compounded medications and ensure their proper usage and storage.
An Unusual Cause of Back Pain in a 10-Year-Old Girl
Authors: Sandelich Stephen Michael , Adirim Terry A.
Published: July 2016

A 10-year-old girl with a 2-week history of atraumatic back pain presented to the emergency department with difficulty ambulating and a history of 2 episodes of urinary incontinence in the past week. Her examination was significant for pain with movement, tenderness to palpation in the lower thoracic spine, and no neurological deficits. In this case, the child was found to have a Schmorl node at T8 in the superior aspect of the vertebral body. Schmorl nodes are protrusions of the cartilage of the intervertebral disc through the vertebral body endplate and into the adjacent that is more commonly reported in the adult population. In this child, radiographic findings were normal, with no evidence of the Schmorl node. The diagnosis was made by magnetic resonance imaging. The child's symptoms significantly resolved with ibuprofen anti-inflammatory therapy. In children with atraumatic back pain lasting greater than 2 weeks with a sudden increase in severity and associated with a neurological deficit, advanced imaging is strongly recommended.
Bloodstream Infections in Patients With Intestinal Failure Presenting to a Pediatric Emergency Department With Fever and a Central Line
Authors: Szydlowski Ellen G. , Rudolph Jeffrey A. , Vitale Melissa A. , Zuckerbraun Noel S.
Published: July 2016

Objective

Previous small studies have found a high occurrence of bloodstream infections (BSIs) in patients with intestinal failure, and these rates are higher than reported rates in other pediatric populations with central lines. The primary study objective was to describe the occurrence of BSIs in patients with intestinal failure who present to the pediatric emergency department (ED) with fever.

Methods

This 5-year retrospective chart review included febrile patients with intestinal failure and central lines who presented to the Children's Hospital of Pittsburgh ED between 2006 and 2011. Each febrile episode was analyzed at the visit level.

Results

During the study, 72 patients with 519 febrile episodes were identified. Central blood cultures were obtained in 93% (480/519) of episodes and 69% (330/480) were positive. Of all BSIs, 38% (124/330) were polymicrobial, 32% (105/330) were a single gram-positive organism, 25% (84/330) were a single gram-negative organism, and 5% (17/330) were a single fungal organism. Of the bacterial pathogens, 48% (223/460) were gram-negative. Overall, 60% were enteric organisms.

Conclusions

Pediatric patients with intestinal failure and central lines have a high occurrence of BSIs with 69% of cultures positive in this study of ED febrile episodes. In contrast to reports in other populations with central lines, BSI occurrence in patients with intestinal failure and fever is higher and larger proportions are gram-negative and enteric organisms. For these patients, we recommend central and peripheral blood cultures, empiric broad spectrum antibiotics targeting gram-negative and enteric organisms, and hospital admission.
A Decade of Antiretroviral Therapy Scale-up in Mozambique: Evaluation of Outcome Trends and New Models of Service Delivery Among More Than 300,000 Patients Enrolled During 2004—2013
Authors: Auld Andrew F. , Shiraishi Ray W. , Couto Aleny , Mbofana Francisco , Colborn Kathryn , Alfredo Charity , Ellerbrock Tedd V. , Xavier Carla , Jobarteh Kebba
Published: July 2016

Background:

During 2004–2013 in Mozambique, 455,600 HIV-positive adults (≥15 years old) initiated antiretroviral therapy (ART). We evaluated trends in patient characteristics and outcomes during 2004–2013, outcomes of universal treatment for pregnant women (Option B+) implemented since 2013, and effect on outcomes of distributing ART to stable patients through Community ART Support Groups (CASG) since 2010.

Methods:

Data for 306,335 adults starting ART during 2004–2013 at 170 ART facilities were analyzed. Mortality and loss to follow-up (LTFU) were estimated using competing risks models. Outcome determinants were estimated using proportional hazards models, including CASG participation as a time-varying covariate.

Results:

Compared with ART enrollees in 2004, enrollees in 2013 were more commonly female (55% vs. 73%), more commonly pregnant if female (<1% vs. 30%), and had a higher median baseline CD4 count (139 vs. 235/μL). During 2004–2013, observed 6-month mortality declined from 7% to 2% but LTFU increased from 24% to 30%. Pregnant women starting ART with CD4 count >350/μL and WHO stage I/II under Option B+ guidelines in 2013 had low 6-month mortality (0.1%) but high 6-month LTFU (38%). During 2010–2013, 6766 patients joined CASGs. In multivariable analysis, compared with nonparticipation in CASG, CASG participation was associated with 35% lower LTFU but similar mortality.

Conclusions:

Initiation of ART at earlier disease stages in later calendar years might explain observed declines in mortality. Retention interventions are needed to address trends of increasing LTFU overall and the high LTFU among Option B+ pregnant women specifically. Further expansion of CASG could help reduce LTFU.
Enhancing PrEP Access for Black and Latino Men Who Have Sex With Men
Authors: Lelutiu-Weinberger Corina , Golub Sarit A.
Published: July 2016

Objective:

Implementation of HIV pre-exposure prophylaxis (PrEP) programs for populations with highest incidence is critical to reducing new infections in the United States. Black and Latino men who have sex with men (BLMSM) are disproportionately burdened by HIV. We examined differences in perceived barriers and facilitators to PrEP access for BLMSM compared with other men who have sex with men (MSM).

Method:

MSM who met the Centers for Disease Control and Prevention criteria for PrEP (n = 491) completed measures of barriers and facilitators to PrEP at the systems, provider, and individual levels. Multivariate analyses examined differences by race/ethnicity, adjusting for other sociodemographic factors.

Results:

Compared with other MSM, BLMSM (56% of the sample) were more likely to have public insurance and to access health care via public clinics [adjusted odds ratio(aOR) 3.2, P < 0.001; aOR 2.4, P < 0.01]. BLMSM were more likely to regard having to talk to their doctor about their sex life as a barrier to PrEP (aOR 3.7, P < 0.001) and were less likely to endorse agency in medical decision making (aOR 0.58, P < 0.001). BLMSM were more likely to report PrEP stigma (aOR 2.3, P < 0.001) and concerns regarding PrEP efficacy (aOR 1.6, P < 0.05). BLMSM were more likely to consider access to free sexual health care (aOR 2.1, P < 0.01) and additional supportive services, eg, counseling (aOR 3.1, P < 0.001) or text-based support (aOR 2.9, P < 0.001) to be significant facilitators of PrEP use.

Conclusions:

Findings suggest specific points of multilevel intervention to increase PrEP access for BLMSM and increase representation of BLMSM along the PrEP continuum of care.
Foodborne viral infections
Authors: Iturriza-Gomara Miren , O’Brien Sarah J.
Published: July 2016

Purpose of review

The aim of the study was to provide an update on foodborne viral infections describing illness burden, the main aetiological agents (enteric viruses, hepatitis viruses and emerging and zoonotic viruses) and advances in virus detection in foods.

Recent findings

Norovirus (NoV) is the most common viral foodborne pathogen globally (125 million cases and 35 000 deaths). The role of the asymptomatic food handlers in contributing to NoV outbreaks is becoming increasingly clear, with up to one-quarter of outbreaks attributable to them. Handwashing with soap and water remains the best method for removing NoV from fingers. Risk assessment for transmission of emerging viruses through the food chain should include consideration of all means by which food could post a hazard, that is not just consumption. New technologies have demonstrated the widespread nature of viral contamination in the food chain, but this does not necessarily correlate with the risk of disease. Finally, understanding people's knowledge and behaviour is just as important as understanding virus characteristics and epidemiology when assessing risks of foodborne transmission.

The predominant viruses transmitted through food tend to be those for which humans are the natural hosts, so that effective control measures need to prevent exposure of foods to human faeces.
Animal models for cancer cachexia
Authors: Ballarò Riccardo , Costelli Paola , Penna Fabio
Published: July 2016

Purpose of review

Cancer cachexia is a frequent syndrome that affects patient quality of life, anticancer treatment effectiveness, and overall survival. The lack of anticancer cachexia therapies likely relies on the complexity of the syndrome that renders difficult to design appropriate clinical trials and, conversely, on the insufficient knowledge of the underlying pathogenetic mechanisms. The aim of this review is to collect the most relevant latest information regarding cancer cachexia with a special focus on the experimental systems adopted for modeling the disease in translational studies.

Recent findings

The scenario of preclinical models for the study of cancer cachexia is not static and is rapidly evolving in parallel with new prospective treatment options. The well established syngeneic models using rodent cancer cells injected ectopically are now used alongside new ones featuring orthotopic injection, human cancer cell or patient-derived xenograft, or spontaneous tumors in genetically engineered mice.

The use of more complex animal models that better resemble cancer cachexia, ideally including also the administration of chemotherapy, will expand the understanding of the underlying mechanisms and will allow a more reliable evaluation of prospective drugs for translational purposes.
Quantification of β-Cell Mass in Intramuscular Islet Grafts Using Radiolabeled Exendin-4
Authors: Espes Daniel , Selvaraju Ramkumar , Velikyan Irina , Krajcovic Martin , Carlsson Per-Ola , Eriksson Olof
Published: July 2016

Background

There is an increasing interest in alternative implantation sites to the liver for islet transplantation. Intramuscular implantation has even been tested clinically. Possibilities to monitor β-cell mass would be of huge importance not only for the understanding of islet engraftment but also for the decision of changing the immunosuppressive regime. We have therefore evaluated the feasibility of quantifying intramuscular β-cell mass using the radiolabeled glucagon like peptide-1 receptor agonist DO3A-VS-Cys40-Exendin-4.

Methods

One hundred to 400 islets were transplanted to the abdominal muscle of nondiabetic mice. After 3 to 4 weeks, 0.2 to 0.5 MBq [177Lu]DO3A-VS-Cys40-Exendin-4 was administered intravenously. Sixty minutes postinjection abdominal organs and graft bearing muscle were retrieved, and the radioactive uptake measured in a well counter within 10 minutes. The specific uptake in native and transplanted islets was assessed by autoradiography. The total insulin-positive area of the islet grafts was determined by immunohistochemistry.

Results

Intramuscular islet grafts could easily be visualized by this tracer, and the background uptake was very low. There was a linear correlation between the radioactivity uptake and the number of transplanted islets, both for standardized uptake values and the total radiotracer uptake in each graft (percentage of injected dose). The quantified total insulin area of surviving β cells showed an even stronger correlation to both standardized uptake values (R = 0.96, P = 0.0002) and percentage of injected dose (R = 0.88, P = 0.0095). There was no correlation to estimated α cell mass.

Conclusions

[177Lu]DO3A-VS-Cys40-Exendin-4 could be used to quantify β-cell mass after experimental intramuscular islet transplantation. This technique may well be transferred to the clinical setting by exchanging Lutetium-177 radionuclide to a positron emitting Gallium-68.
The Kupffer Cell Number Affects the Outcome of Living Donor Liver Transplantation from Elderly Donors
Authors: Hidaka Masaaki , Eguchi Susumu , Takatsuki Mitsuhisa , Soyama Akihiko , Ono Shinichiro , Adachi Tomohiko , Natsuda Koji , Kugiyama Tota , Hara Takanobu , Okada Satomi , Imamura Hajime , Miuma Satoshi , Miyaaki Hisamitsu
Published: July 2016

Background

There have been no previous reports how Kupffer cells affect the outcome of living donor liver transplantation (LDLT) with an elderly donor. The aim of this study was to elucidate the influence of Kupffer cells on LDLT.

Methods

A total of 161 adult recipients underwent LDLT. The graft survival, prognostic factors for survival, and graft failure after LDLT were examined between cases with a young donor (<50, n = 112) and an elderly donor (≥50, N = 49). The Kupffer cells, represented by CD68-positive cell in the graft, were examined in the young and elderly donors.

Results

In a multivariable analysis, a donor older than 50 years, sepsis, and diabetes mellitus were significant predictors of graft failure after LDLT. The CD68 in younger donors was significantly more expressed than that in elderly donors. The group with a less number of CD68-positive cells in the graft had a significantly poor survival in the elderly donor group and prognostic factor for graft failure.

Conclusions

The worse outcome of LDLT with elderly donors might be related to the lower number of Kupffer cells in the graft, which can lead to impaired recovery of the liver function and may predispose patients to infectious diseases after LDLT.
Treatment approaches in motor neurone disease
Authors: Dharmadasa Thanuja , Matamala José M. , Kiernan Matthew C.
Published: July 2016

Purpose of review

Although there is no cure for motor neurone disease (MND), the advent of multidisciplinary care and neuroprotective agents has improved treatment interventions and enhanced quality of life for MND patients and their carers.

Recent findings

Evidence-based multidisciplinary care, respiratory management and disease-modifying therapy have improved the outcomes of patients diagnosed with MND. Supportive approaches to nutritional maintenance and optimization of symptomatic treatments, including management of communication and neuropsychiatric issues, improve the quality of life for MND patients.

Recent progress in the understanding of the clinical, pathophysiological and genetic heterogeneity of MND has improved the approach of clinicians to treatment. Notwithstanding improvement to care and quality of life, survival benefit has become evident with the advent of a multidisciplinary care framework, early treatment with riluzole and noninvasive ventilation. Weight maintenance remains critical, with weight loss associated with more rapid disease progression. The end-of-life phase is poorly defined and treatment is challenging, but effective symptom control through palliative care is achievable and essential. Encouragingly, current progress of clinical trials continues to close the gap towards the successful development of curative treatment in MND.
Nonadaptive Radiation: Pervasive diet specialization by drift in scale insects?
Authors: Hardy Nate B , Peterson Daniel A , Normark Benjamin B
Published: July 2016

At least half of metazoan species are herbivorous insects. Why are they so diverse? Most herbivorous insects feed on few plant species, and adaptive host specialization is often invoked to explain their diversification. Nevertheless, it is possible that the narrow host ranges of many herbivorous insects are non-adaptive. Here, we test predictions of this hypothesis with comparative phylogenetic analyses of scale insects, a group for which there appears to be few host-use tradeoffs that would select against polyphagy, and for which passive wind-dispersal should make host specificity costly. We infer a strong positive relationship between host range and diversification rate, and a marked asymmetry in cladogenetic changes in diet breadth. These results are consonant with a system of pervasive non-adaptive host specialization in which small, drift-and extinction-prone populations are frequently isolated from persistent and polyphagous source populations. They also contrast with the negative relationship between diet breadth and taxonomic diversification that has been estimated in butterflies, a disparity which likely stems from differences in the average costs and benefits of host specificity and generalism in scale insects vs. butterflies. Our results indicate the potential for non-adaptive processes to be important to diet-breadth evolution and taxonomic diversification across herbivorous insects.
A cascade of destabilizations: combiningWolbachiaand Allee effects to eradicate insect pests
Authors: Blackwood Julie C. , Vargas Roger , Fauvergue Xavier
Published: July 2016

The management of insect pests has long been dominated by the use of chemical insecticides, with the aim of instantaneously killing enough individuals to limit their damage. To minimize unwanted consequences, environmentally-friendly approaches have been proposed that utilize biological control and take advantage of intrinsic demographic processes to reduce pest populations.

We address the feasibility of a novel pest management strategy based on the release of insects infected withWolbachia, which causes cytoplasmic incompatibilities in its host population, into a population with a pre-existing Allee effect. We hypothesize that the transient decline in population size caused by a successful invasion ofWolbachiacan bring the population below its Allee threshold and, consequently, trigger extinction.

We develop a stochastic population model that accounts forWolbachia-induced cytoplasmic incompatibilities in addition to an Allee effect arising from mating failures at low population densities. Using our model, we identify conditions under which cytoplasmic incompatibilities and Allee effects successfully interact to drive insect pest populations toward extinction. Based on our results, we delineate control strategies based on introductions ofWolbachia-infected insects.

We extend this analysis to evaluate control strategies that implement successive introductions of two incompatibleWolbachiastrains. Additionally, we consider methods that combineWolbachiainvasion with mating disruption tactics to enhance the pre-existing Allee effect.

We demonstrate that Wolbachia-induced cytoplasmic incompatibility and the Allee effect act independently from one another: the Allee effect does not modify theWolbachia-invasion threshold, and cytoplasmic incompatibilities only have a marginal effect on the Allee threshold. However, the interaction of these two processes can drive even large populations to extinction. The success of this method can be amplified by the introduction of multipleWolbachiacytotypes as well as the addition of mating disruption.

Our study extends the existing literature by proposing the use ofWolbachiaintroductions to capitalize on pre-existing Allee effects and consequently eradicate insect pests. More generally, it highlights the importance of transient dynamics, and the relevance of manipulating a cascade of destabilizatons for pest management.
On phylogenetic branch lengths distribution and the late acquistion of mitochondria
Authors: Pittis Alexandros A. , Gabaldón Toni
Published: July 2016

In a recent article, Martin et. al. [1] criticize several methodological aspects of our recent study on the timing of the acquisition of mitochondria [2]. Here we show that our results are independent of the model-based partitioning of the data. In addition, we assess the robustness of our inferences by analyzing data from Martin et. al.
Quantitative, image-based phenotyping methods provide insight into spatial and temporal dimensions of plant disease
Authors: Mutka Andrew M. , Fentress Sarah J. , Sher Joel W. , Berry Jeffrey C. , Pretz Chelsea , Nusinow Dmitri A. , Bart Rebecca
Published: July 2016

Plant disease symptoms exhibit complex spatial and temporal patterns that are challenging to quantify. Image-based phenotyping approaches enable multi-dimensional characterization of host-microbe interactions and are well suited to capture spatial and temporal data that are key to understanding disease progression. We applied image-based methods to investigate cassava bacterial blight, which is caused by the pathogenXanthomonas axonopodispv.manihotis(Xam). We generatedXamstrains in which individual predicted type III effector (T3E) genes were mutated and applied multiple imaging approaches to investigate the role of these proteins in bacterial virulence. Specifically, we quantified bacterial populations, water-soaking disease symptoms, and pathogen spread from the site of inoculation over time for strains with mutations inavrBs2,xopX, andxopKas compared to wild-typeXam. ΔavrBs2and ΔxopXboth showed reduced growth in planta and delayed spread through the vasculature system of cassava. ΔavrBs2exhibited reduced water-soaking symptoms at the site of inoculation. In contrast, ΔxopKexhibited enhanced induction of disease symptoms at the site of inoculation but reduced spread through the vasculature. Our results highlight the importance of adopting a multi-pronged approach to plant disease phenotyping to more fully understand the roles of T3Es in virulence. Finally, we demonstrate that the approaches used in this study can be extended to many host-microbe systems and increase the dimensions of phenotype that can be explored.

Novel, image-based phenotyping methods enhance characterization of plant-pathogen interactions.
Massively multiplex single-cell Hi-C
Authors: Ramani Vijay , Deng Xinxian , Gunderson Kevin L , Steemers Frank J , Disteche Christine M , Noble William S , Duan Zhijun , Shendure Jay
Published: July 2016

We present combinatorial single cell Hi-C, a novel method that leverages combinatorial cellular indexing to measure chromosome conformation in large numbers of single cells. In this proof-of-concept, we generate and sequence combinatorial single cell Hi-C libraries for two mouse and four human cell types, comprising a total of 9,316 single cells across 5 experiments. We demonstrate the utility of single-cell Hi-C data in separating different cell types, identify previously uncharacterized cell-to-cell heterogeneity in the conformational properties of mammalian chromosomes, and demonstrate that combinatorial indexing is a generalizable molecular strategy for single-cell genomics.
High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida
Authors: Starrett James , Derkarabetian Shahan , Hedin Marshal , Bryson Robert W. , McCormack John E. , Faircloth Brant C.
Published: July 2016

Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite this applied importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have confounded these attempts. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved genomic regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, even down to the level of species differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.
A Rationally Designed Aminoacyl-tRNA Synthetase for Genetically Encoded Fluorescent Amino Acids
Authors: Steinberg Ximena , Galpin Jason , Nasir Gibran , Sepulveda-Ugarte Jose , Sepúlveda Romina V. , Gonzalez-Nilo Fernando , Islas Leon D. , Ahern Christopher A. , Brauchi Sebastian
Published: July 2016

The incorporation of non-canonical amino acids into proteins has emerged as a promising strategy to manipulate and study protein structure-function relationships with superior precisionin vitroandin vivo. To date, fluorescent non-canonical amino acids (f-ncAA) have been successfully incorporated in proteins expressed in bacterial systems,Xenopusoocytes, and HEK-293T cells. Here, we describe the rational generation of an orthogonal aminoacyltRNA synthetase based on theE. colityrosine synthetase that is capable of encoding the f-ncAA tyr-coumarin in HEK-293T cells.
Neuroendocrine Modulation Sustains theC. elegansForward Motor State
Authors: Lim Maria A. , Chitturi Jyothsna , Laskova Valeriya , Meng Jun , Findeis Daniel , Wiekenberg Anne , Mulcahy Ben , Luo Linjiao , Li Yan , Lu Yangning , Hung Wesley , Qu Yixin , Ho Chi-Yip , Holmyard Douglas , Ji Ni , McWhirter Rebecca , Samuel Aravinthan D. T. , Miller David M. , Schnabel Ralf , Calarco John A. , Zhen Mei
Published: July 2016

Neuromodulators shape neural circuit dynamics. Combining electron microscopy, genetics, transcriptome profiling, calcium imaging, and optogenetics, we discovered a peptidergic neuron that modulatesC. elegansmotor circuit dynamics. The Six/SO-family homeobox transcription factor UNC-39 governs lineage-specific neurogenesis to give rise to a neuron RID. RID bears the anatomic hallmarks of a specialized endocrine neuron: it harbors near-exclusive dense core vesicles that cluster periodically along the axon, and expresses multiple neuropeptides, including the FMRF-amide-related FLP-14. RID activity increases during forward movement. Ablating RID reduces the sustainability of forward movement, a phenotype partially recapitulated by removing FLP-14. Optogenetic depolarization of RID prolongs forward movement, an effect reduced in the absence of FLP-14. Together, these results establish the role of a neuroendocrine cell RID in sustaining a specific behavioral state inC. elegans.
Probabilistic adaptation in changing microbial environments
Authors: Katz Yarden , Springer Michael
Published: July 2016

Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the animal host’s behavior, diet, health and microbiota composition. Microbial cells that are able to anticipate these fluctuations by exploiting this structure would likely gain a fitness advantage, by adapting their internal state in advance. We propose that the problem of adaptive growth in these structured changing environments can be viewed as probabilistic inference. We analyze environments that are “meta-changing”: where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering) for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.
The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core
Authors: Deco Gustavo , Kringelbach Morten L. , Jirsa Viktor K. , Ritter Petra
Published: July 2016

In the human brain, spontaneous activity during resting state consists of rapid transitions between functional network states over time but the underlying mechanisms are not understood. We use connectome based computational brain network modeling to reveal fundamental principles of how the human brain generates large-scale activity observable by noninvasive neuroimaging. By including individual structural and functional neuroimaging data into brain network models we construct personalized brain models. With this novel approach, we reveal that the human brain during resting state operates at maximum metastability, i.e. in a state of maximum network switching. In addition, we investigate cortical heterogeneity across areas. Optimization of the spectral characteristics of each local brain region revealed the dynamical cortical core of the human brain, which is driving the activity of the rest of the whole brain. Personalized brain network modelling goes beyond correlational neuroimaging analysis and reveals non-trivial network mechanisms underlying non-invasive observations. Our novel findings significantly pertain to the important role of computational connectomics in understanding principles of brain function.
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
Authors: Didelot Xavier , Fraser Christophe , Gardy Jennifer , Colijn Caroline
Published: July 2016

Genomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in. Here we extend this approach and show that it can be applied to partially sampled and ongoing outbreaks. This requires computing the correct probability of an observed transmission tree and we herein demonstrate how to do this for a large class of epidemiological models. We also demonstrate how the branch colouring approach can incorporate a variable number of unique colours to represent unsampled intermediates in transmission chains. The resulting algorithm is a reversible jump Monte-Carlo Markov Chain, which we apply to both simulated data and real data from an outbreak of tuberculosis. By accounting for unsampled cases and an outbreak which may not have reached its end, our method is uniquely suited to use in a public health environment during real-time outbreak investigations. We implemented our technique in an R package called TransPhylo, which is freely available fromhttps://github.com/xavierdidelot/TransPhylo.
Morphological structure of ant assemblages in tropical and temperate forests
Authors: Silva Rogério R. , Toro Israel Del , Brandão Carlos Roberto F. , Ellison Aaron M.
Published: July 2016

Morphological variation in co-occurring species often is used to infer species assembly rules and other processes structuring ecological assemblages. We compared the morphological structure of ant assemblages in two biogeographic regions along two extensive latitudinal gradients to examine common patterns and unique characteristics of trait distribution. We sampled ant assemblages along extensive latitudinal gradients in Tropical Atlantic Forest in eastern Brazil and temperate forests in the eastern United States. We quantified 14 morphological traits related to the ecology and life history of each of 599 ant species and defined the morphological space occupied by different ant assemblages. Null models were used to test whether tropical and temperate ant assemblages differed from random expectation in morphological structure. Correlations between traits and climate were used to infer associations between habitat characteristics and morphological space occupied by ant assemblages. Tropical ant assemblages had higher morphological diversity and variation in the space of occupied morphospace, whereas temperate assemblages had higher variance in size. Although tropical ant assemblages had smaller morphological distances among species, species packing (i.e., mean nearest-neighbor distance) did not differ between regions. Null model analysis revealed scant evidence of habitat filtering or niche differentiation within assemblages. Different traits had different means, variances, skewness, and kurtosis values along each environmental gradient. Mean trait values within assemblages were associated mainly with region and correlated with temperature but trait variances had more complex responses to climate, including interactions between temperature and precipitation in the models. The higher functional diversity in tropical ant assemblages occurs by expansion of the morphospace rather than through an increase in species packing. Different traits vary independently along environmental gradients. Analysis of individual traits together with categorization of the moments of trait distributions (statistical central tendencies) provide new directions for quantifying morphological diversity in ant assemblages.
Genome size variation and species diversity in salamanders
Authors: Herrick John , Sclavi Bianca
Published: July 2016

Salamanders (Urodela) have among the largest vertebrate genomes, ranging in size from 10 to 120 pg. Although changes in genome size often occur randomly and in the absence of selection pressure, non-random patterns of genome size variation are evident among specific vertebrate lineages. Several reports suggest a relationship between species richness and genome size, but the exact nature of that relationship remains unclear both within and across different taxonomic groups. Here we report i) a negative relationship between haploid genome size (C-value) and species richness at the family taxonomic level in salamander clades; ii) a correlation of C-value and species richness with clade crown-age but not with diversification rates; iii) strong associations between C-value and either geographical area or climatic niche rate. Finally, we report a relationship between C-value diversity and species diversity at both the family and genus level clades in urodeles.
Patterns of individual variation in visual pathway structure and function in the sighted and blind
Authors: Aguirre Geoffrey K. , Datta Ritobrato , Benson Noah C. , Prasad Sashank , Jacobson Samuel G. , Cideciyan Artur V. , Bridge Holly , Watkins Kate E. , Butt Omar H. , Dain Alexsandra S. , Brandes Lauren , Gennatas Efstathios D.
Published: July 2016

Many structural and functional brain alterations accompany blindness, with substantial individual variation in these effects. In normally sighted people, there is correlated individual variation in some visual pathway structures. Here we examined if the changes in brain anatomy produced by blindness alter the patterns of anatomical variation found in the sighted. We derived eight measures of central visual pathway anatomy from a structural image of the brain from 59 sighted and 53 blind people. These measures showed highly significant differences in mean size between the sighted and blind cohorts. When we examined the measurements across individuals within each group we found three clusters of correlated variation, with V1 surface area and pericalcarine volume linked, and independent of the thickness of V1 cortex. These two clusters were in turn relatively independent of the volumes of the optic chiasm and lateral geniculate nucleus. This same pattern of variation in visual pathway anatomy was found in the sighted and the blind. Anatomical changes within these clusters were graded by the timing of onset of blindness, with those subjects with a post-natal onset of blindness having alterations in brain anatomy that were intermediate to those seen in the sighted and congenitally blind. Many of the blind and sighted subjects also contributed functional MRI measures of cross-modal responses within visual cortex, and a diffusion tensor imaging measure of fractional anisotropy within the optic radiations and the splenium of the corpus callosum. We again found group differences between the blind and sighted in these measures. The previously identified clusters of anatomical variation were also found to be differentially related to these additional measures: across subjects, V1 cortical thickness was related to cross-modal activation, and the volume of the optic chiasm and lateral geniculate was related to fractional anisotropy in the visual pathway. Our findings show that several of the structural and functional effects of blindness may be reduced to a smaller set of dimensions. It also seems that the changes in the brain that accompany blindness are on a continuum with normal variation found in the sighted.
Global population divergence and admixture of the brown rat (Rattus norvegicus)
Authors: Puckett Emily E. , Park Jane , Combs Matthew , Blum Michael J. , Bryant Juliet E. , Caccone Adalgisa , Costa Federico , Deinum Eva E. , Esther Alexandra , Himsworth Chelsea G. , Keightley Peter D. , Ko Albert , Lundkvist Åke , McElhinney Lorraine M. , Morand Serge , Robins Judith , Russell James , Strand Tanja M. , Suarez Olga , Yon Lisa , Munshi-South Jason
Published: July 2016

Once restricted to northern China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution due to the evolution of commensalism with humans. In contrast to black rats and the house mouse, which have tracked the regional and global development of human agricultural settlements, brown rats do not appear in the European historical record until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade and modern sea-faring. We inferred the global phylogeography of brown rats using 32k SNPs to reconstruct invasion routes from estimates of population divergence and admixture. Globally, we detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Rapid westward expansion resulted in the colonization of Europe from which subsequent colonization of Africa, the Americas, and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering found both between and within our sampling sites underscored the extent to which urban heterogeneity can shape the genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants despite continual global transport, suggesting that recruitment into established populations is limited. Understanding the global population structure ofR. norvegicusoffers novel perspectives on the forces driving the spread of zoonotic disease, and yields greater capacity to develop targeted rat eradication programs.
An introduction to linear stability analysis for deciphering spatial patterns in signaling networks
Authors: Nirody Jasmine A. , Rangamani Padmini
Published: July 2016

Mathematical modeling is now used commonly in the analysis of signaling networks. With advances in high resolution microscopy, the spatial location of different signaling molecules and the spatio-temporal dynamics of signaling microdomains are now widely acknowledged as key features of biochemical signal transduction. Reaction-diffusion mechanisms are commonly used to model such features, often with a heavy reliance on numerical simulations to obtain results. However, simulations are parameter dependent and may not be able to provide an understanding of the full range of the system responses. Analytical approaches on the other hand provide a framework to study the entire phase space. In this tutorial, we provide a largely analytical method for studying reaction-diffusion models and analyzing their stability properties. Using two representative biological examples, we demonstrate how this approach can guide experimental design.