bluuebunny/crossref_metadata_2025 huggingface dataset:
The Toxin Antitoxin MazEF DrivesStaphylococcus aureusChronic Infection
Authors: Ma Dongzhu , Mandell Jonathan B. , Donegan Niles P. , Cheung Ambrose L. , Ma Wanyan , Rothenberger Scott , Shanks Robert M. Q. , Richardson Anthony R. , Urish Kenneth L.
Published: July 2019

Staphylococcus aureusis the major organism responsible for surgical implant infections. Antimicrobial treatment of these infections often fails leading to expensive surgical intervention and increased risk of mortality to the patient. The challenge in treating these infections is associated with the high tolerance ofS. aureusbiofilm to antibiotics. MazEF, a toxin-antitoxin system, is thought to be an important regulator of this phenotype, but its physiological function inS. aureusis controversial. Here, we examined the role of MazEF in developing chronic infections by comparing growth and antibiotic tolerance phenotypes in threeS. aureusstrains to their corresponding strains with disruption ofmazFexpression. Strains lackingmazFproduction showed increased biofilm growth, and decreased biofilm antibiotic tolerance. Deletion oficaADBCin themazF::tn background suppressed the growth phenotype observed withmazF-disrupted strains, suggesting the phenotype wasica-dependent. We confirmed these phenotypes in our murine animal model. Loss ofmazFresulted in increased bacterial burden and decreased survival rate compared to its wild-type strain demonstrating that loss of themazFgene caused an increase inS. aureusvirulence. Although lack ofmazFgene expression increasedS. aureusvirulence, it was more susceptible to antibioticsin vivo. Combined, the ability ofmazFto inhibit biofilm formation and promote biofilm antibiotic tolerance plays a critical role in transitioning from an acute to chronic infection that is difficult to eradicate with antibiotics alone.

Importance

Surgical infections are one of the most common types of infections obtained in a hospital.Staphylococcus aureusis the most common pathogen associated with this infection. These infections are resilient and difficult to eradicate as the bacteria form a biofilm, a community of bacteria held together by an extracellular matrix. Compared to bacteria floating in liquid, bacteria in a biofilm are more resistant to antibiotics. The mechanism behind how bacteria develop this resistance and establish a chronic infection is unknown. We demonstrate thatmazEF, a toxin-antitoxin gene, inhibits biofilm formation and promotes biofilm antibiotic tolerance which allowsS. aureusto transition from an acute to chronic infection that cannot be eradicated with antibiotics but is less virulent. This gene not only makes the bacteria more tolerant to antibiotics but makes the bacteria more tolerant to the host.
Prevalence of Alcohol use during pregnancy and its association with partner alcohol use in East Africa: systematic review and meta-analysis
Authors: Dargie Abate , Eshetie Yossef , Asmare Yared , Shibabaw Wendimeneh , Dagne Kefyalew
Published: July 2019

Introduction

maternal alcohol beverages consumption (any amount) during pregnancy can result in multiple major health and social problems both for the mother and fetus; including miscarriage, stillbirth, low birth weight, and prematurity. At the regional and national level, alcohol use prevalence data is a use full indicator for maternal and child health.

Methods

the researchers were searched for studies using a computerized search engine, main electronic databases, and other applicable sources. Observational studies (case-control, crosssectional and cohort) which assess the prevalence of alcohol use and associated factors among pregnant mothers in East Africa were eligible. Data was extracted thoroughly by two authors independently and screened for eligibility. The Pooled prevalence of alcohol use during pregnancy and its association with partner alcohol use was determined by using Epi data version 14 statistical software.

Results

the study included eighteen studies with the total sample size of 41,022 and The overall pooled prevalence of alcohol use during pregnancy from the random effects method was found to be 18.85% (95% CI; 11.26, 26.44). The overall weighted odds ration revealed that pregnant women partners’ alcohol use did not have a significant association with study subjects alcohol use during pregnancy; i.e. OR=0.32(95% CI: −0.39, 1.03).

Conclusions

The overall alcohol use (any amount) during pregnancy is higher in magnitude and pregnant mothers who had alcohol user partner had no association with their use of alcohol beverages. The prevalence of alcohol use during pregnancy may be underestimated in the current study due to social desirability bias. Since related study articles were found only in four East African countries, the region may be under-represented due to the limited number of studies included.
Seasonal diversity of soil microarthropods in two different vegetable plots of Aligarh-India
Authors: Abbas Mohammad Jalaluddin , Parwez Hina
Published: July 2019

Soil microarthropods are intimately linked with health and fertility of soil as well as plant productivity. In India, despite their rich faunal diversity, information on soil microarthropods diversity and interactions with variety of edaphic factors is extremely limited. The present study has been carried out to observe seasonal diversity of soil microarthropods in two different vegetable plots at Aligarh. The two vegetable plots chosen in this study where predominantly Tomato (Lycopersicom esculentum) and Brinjal (Solanum melongena, family-Solaneceae) have been grown and sapling has been sown in the month of April when plants attained a height of approximately 6″. The samples were collected randomly from a depth of 5cm. @ of four samples per month for a period of one year. All microarthropods extracted with the help of Tullgren funnel apparatus. Among soil microarthropods collected, Collembolans have highest average monthly density (15.20 inds./sample) in brinjal plot and greatest abundance (18.7inds./sample) in tomato plot. A highly significant negative correlation was recorded between Collembolans population with reference to soil temperature (r = −0.867, P<0.05), whereas available nitrogen showed a positive correlation (r = 0.847, P>0.05). Interestingly, at neutral pH level, the highest population of Collembolans as well as Acari(mites) were recorded. During spring and winter months, there was a peak population buildup of Collembola and Acarina, whereas a sharp decline was recorded in summer months. So, this study clearly establishes that habitat difference as well as edaphic factors plays an important role along with seasonal parameters on their diversity.
Correlation between Retinal Ganglion Cell Loss and Nerve Crush Force-Impulse Established with Instrumented Tweezers in Mice
Authors: Liu Xiaorong , Feng Liang , Shinde Ishan , Cole James D. , Troy John B. , Saggere Laxman
Published: July 2019

Objectives

Rodent models of optic nerve crush (ONC) have often been used to study degeneration and regeneration of retinal ganglion cells (RGCs) and their axons as well as the underlying molecular mechanisms. However, ONC results from different laboratories exhibit a range of RGC injury with varying degree of axonal damage. We developed an instrumented tweezers to measure optic nerve (ON) crush forces in real time and studied the correlation between RGC axon loss and force-impulse, the product of force and duration, applied through the instrumented tweezers in mice.

Methods

A pair of standard self-closing #N7 tweezers were instrumented with miniature foil strain gauges at optimal locations on both tweezer arms. The instrumented tweezers were capable of recording the tip closure forces in the form of voltages, which were calibrated through load cells to corresponding tip closure forces over the operating range. Using the instrumented tweezers, the ONs of multiple mice were crushed with varied forces and durations and the axons in the immunostained sections of the crushed ONs were counted.

Results

We found that the surviving axon density correlated with crush force, with longer duration and stronger crush forces producing consistently more axon damage.

Discussion

The instrumented tweezers enable a simple technique for measurement of ONC forces in real-time for the first time. Using the instrumented tweezers, experimenters can quantify crush forces during ONC to produce consistent and predictable post-crush cell death. This should permit future studies a way to produce nerve damage more consistently than is available now.
Deep learning reveals hidden variables underlying NF-κB activation in single cells
Authors: Patel Parthiv , Drayman Nir , Liu Ping , Bilgic Mustafa , Tay Savaş
Published: July 2019

Individual cells show great heterogeneity when responding to environmental cues. For example, under cytokine stimulation some cells activate immune signaling pathways while others completely ignore the signal. The underlying sources of cellular variability have been inaccessible due to the destructive nature of experiments. Here we apply deep learning, live-cell analysis, and mechanistic modeling to uncover hidden variables controlling NF-κB activation in single-cells. Our computer-vision algorithm accurately predicts cells that will respond to pro-inflammatory TNF stimulation and shows that single-cell activation is pre-determined by minute amounts of “leaky” nuclear NF-κB localization before stimulation. Theoretical analysis predicts and experiments confirm that the ratio of NF-κB to its inhibitor IκB determines the activation probability of a given cell. Our results demonstrate how computer vision can study living-cells without the use of destructive measurements and settles the question of whether heterogenous NF-κB activation is controlled by pre-existing deterministic variables or purely stochastic ones.
A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep
Authors: Zhao Lele , Lavington Erik , Duffy Siobain
Published: July 2019

Abundant novel circular Rep-encoding ssDNA viruses (CRESS DNA viruses) have been discovered in the past decade, prompting a new appreciation for the ubiquity and genomic diversity of this group of viruses. Although highly divergent in the hosts they infect or are associated with, CRESS DNA viruses are united by the homologous replication-associated protein (Rep). An accurate genealogy of Rep can therefore provide insights into how these diverse families are related to each other. We used a dataset of eukaryote-associated CRESS DNA RefSeq genomes (n=926), which included representatives from all six established families and unclassified species. To assure an optimal Rep genealogy, we derived and tested a bespoke amino acid substitution model (named CRESS), which outperformed existing protein matrices in describing the evolution of Rep. The CRESS model-estimated Rep genealogy resolved the monophyly of Bacilladnaviridae and the reciprocal monophyly of Nanoviridae and the alpha-satellites when trees estimated with general matrices like LG did not. The most intriguing, previously unobserved result is a likely single origin of intron-containing Reps, which causes several geminivirus genera to group with Genomoviridae (bootstrap support 55%, aLRT SH-like support 0.997, 0.91-0.997 in trees estimated with established matrices). This grouping, which eliminates the monophyly of Geminiviridae, is supported by both domains of Rep, and appears to be related to our use of all RefSeq Reps instead of subsampling to get a smaller dataset. In addition to producing a trustworthy Rep genealogy, the derived CRESS matrix is proving useful for other analyses; it best fit alignments of capsid protein sequences from several CRESS DNA families and parvovirus NS1/Rep sequences.
Label-retention expansion microscopy
Authors: Shi Xiaoyu , Li Qi , Dai Zhipeng , Tran Arthur A. , Feng Siyu , Ramirez Alejandro D. , Lin Zixi , Wang Xiaomeng , Chow Tracy T. , Chen Jiapei , Kumar Dhivya , McColloch Andrew R. , Reiter Jeremy F. , Huang Eric J. , Seiple Ian B. , Huang Bo
Published: July 2019

Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with super-resolution Stochastic Optical Reconstruction Microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ.
Natural selection shapes codon usage in the human genome
Authors: Dhindsa Ryan S , Copeland Brett R , Mustoe Anthony M , Goldstein David B
Published: July 2019

Synonymous codon usage has been identified as an important determinant of translational efficiency and mRNA stability in model organisms and human cell lines. However, to date, population genetics studies have failed to observe evolutionary constraint on human codon usage, and synonymous variation has been largely overlooked as a component of human genetic diversity. Using genetic sequencing data from nearly 200,000 individuals, we uncover clear evidence that natural selection optimizes codon content in the human genome. We derive intolerance metrics to quantify gene-level constraint on synonymous variation and demonstrate that dosage-sensitive, DNA damage response, and cell cycle regulated genes are more intolerant to synonymous variation than other genes in the genome. Notably, we illustrate that reductions in codon optimality can attenuate the function of BRCA1. Our results reveal that synonymous mutations likely play an important and underappreciated role in human variation.
A scanning electron microscopy-based screen of leaves ofSolanum pennellii(ac. LA716) xSolanum lycopersicum(cv. M82) introgression lines provides a resource for identification of loci involved in epidermal development in tomato
Authors: Galdon-Armero J. , Arce-Rodriguez M. L. , Martin C.
Published: July 2019

The aerial epidermis of plants plays a major role in their environment interactions, and the development of its cellular components -trichomes, stomata and pavement cells- is still not fully understood. We have performed a detailed screen of the leaf epidermis of two generations of the well-establishedSolanum pennelliiac. LA716 xSolanum lycopersicumcv. M82 introgression line (IL) population using a combination of scanning electron microscopy techniques. Quantification of the trichome and stomatal densities in the ILs revealed 18 genomic regions with a low trichome density and 4 ILs with a high stomatal density. We also found ILs with abnormal proportions of different trichome types and aberrant trichome morphologies. This work has led to the identification of new, unexplored genomic regions with roles in trichome and stomatal formation and provides an important dataset for further studies on tomato epidermal development that is publically available to the research community.
Simultaneous Targeting of XPO1 and BCL2 as an Effective Treatment Strategy for Double-Hit Lymphoma
Authors: Liu Yuanhui , Azizian Nancy G. , Dou Yaling , Pham Lan V. , Li Yulin
Published: July 2019

Double-hit lymphoma (DHL) is among the most aggressive and chemoresistant lymphoma subtypes. DHLs carry genomic abnormalities in MYC, BCL2 and/or BCL6 oncogenes. Due to simultaneous overexpression of these driver oncogenes, DHLs are highly resistant to the frontline therapies. Most DHLs overexpress both MYC and BCL2 driver oncogenes concurrently. We reasoned that simultaneous suppression of the two driver oncogenes would be more effective in eradicating DHLs than inactivation of single oncogene. XPO1 is a receptor for nuclear cytoplasmic transport of protein and RNA species. Recently, XPO1 inhibition was shown to downregulate MYC expression in several cancer cell lines. We therefore examined the role of XPO1 as a therapeutic target in suppressing MYC function and the potential synergistic effects of simultaneous suppression of XPO1 and BCL2 in the treatment of DHL. Here, we demonstrate that XPO1 inhibition abrogates MYC protein expression and induces massive tumor cell apoptosis. Combined use of XPO1 and BCL2 inhibitors is highly effective in eradicating DHL cells in cell culture. Notably, in a mouse model of DHL bearing primary tumor cells derived from lymphoma patients, combined treatment with XPO1 and BCL2 inhibitors blocks tumor progression, prevents brain metastasis, and extends host survival. Thus, our study confirms the simultaneous targeting of MYC and BCL2 driver oncogenes through the combined use of XPO1 and BCL2 inhibitors as a unique approach for the treatment of DHLs.
FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia
Authors: Lin Jianfeng , Le Thuc Vy , Augspurger Katherine , Tritschler Douglas , Bower Raqual , Fu Gang , Perrone Catherine , O’Toole Eileen T. , Mills Kristyn VanderWaal , Dymek Erin , Smith Elizabeth , Nicastro Daniela , Porter Mary E.
Published: July 2019

Ciliary motility depends on both the precise spatial organization of multiple dynein motors within the 96 nm axonemal repeat, and highly coordinated interactions between different dyneins and regulatory complexes located at the base of the radial spokes. Mutations in genes encoding cytoplasmic assembly factors, intraflagellar transport factors, docking proteins, dynein subunits, and associated regulatory proteins can all lead to defects in dynein assembly and ciliary motility. Significant progress has been made in the identification of dynein subunits and extrinsic factors required for pre-assembly of dynein complexes in the cytoplasm, but less is known about the docking factors that specify the unique binding sites for the different dynein isoforms on the surface of the doublet microtubules. We have used insertional mutagenesis to identify a new locus,IDA8/BOP2, required for targeting the assembly of a subset of inner dynein arms to a specific location in the 96 nm repeat.IDA8encodes FAP57/WDR65, a highly conserved WD repeat, coiled coil domain protein. Using high resolution proteomic and structural approaches, we find that FAP57 forms a discrete complex. Cryo-electron tomography coupled with epitope tagging and gold labeling reveal that FAP57 forms an extended structure that interconnects multiple inner dynein arms and regulatory complexes.
NMDAR-dependent emergence of behavioral representation in primary visual cortex
Authors: Puścian Alicja , Benisty Hadas , Higley Michael J.
Published: July 2019

Neocortical sensory areas are generally thought to faithfully represent external stimuli. However, a growing body of evidence suggests that cortical networks exhibit considerable functional plasticity over multiple temporal scales, allowing them to modify their output to reflect ongoing behavioral demands. Nevertheless, the dynamics of sensory and non-sensory representations during acquisition of stimulus-guided behavior are not well understood. We performed longitudinal 2-photon imaging of activity in primary visual cortex (V1) of mice learning a conditioned eyeblink task. We found that both excitatory and inhibitory neurons robustly encode the visual stimulus throughout training despite a significant experience-dependent reduction in response magnitude. In contrast, both pyramidal neurons and parvalbumin-expressing interneurons exhibit emergence of behavioral representation during learning. The plasticity of visual response magnitude and behavioral representation is abolished following loss of NMDA-type glutamate receptors. Overall, our findings demonstrate that V1 networks can dynamically multiplex distinct behaviorally relevant representations over the course of learning.
Optimizing drug infusion schedules towards personalized cancer chronotherapy
Authors: Hill Roger J. W. , Innominato Pasquale F. , Lévi Francis , Ballesta Annabelle
Published: July 2019

Aims

Precision medicine requires accurate technologies for drug administration and proper systems pharmacology approaches for patient data analysis. Here, plasma pharmacokinetics (PK) data of the OPTILIV trial in which cancer patients received oxaliplatin, 5-fluorouracil and irinotecan via chronomodulated schedules delivered by an infusion pump into the hepatic artery were mathematically investigated.

Methods

A pump-to-patient model was designed in order to accurately represent the drug solution dynamics from the pump to the patient blood. It was connected to semi-mechanistic PK models to analyse inter-patient variability in PK parameters.

Results

Large time delays of up to 1h41 between the actual pump start and the time of drug detection in patient blood was predicted by the model and confirmed by PK data. Sudden delivery spike in the patient artery due to glucose rinse after drug administration accounted for up to 10.7% of the total drug dose. New model-guided delivery profiles were designed to precisely lead to the drug exposure intended by clinicians. Next, the complete mathematical framework achieved a very good fit to individual time-concentration PK profiles and concluded that inter-subject differences in PK parameters was the lowest for irinotecan, intermediate for oxaliplatin and the largest for 5-fluorouracil. Clustering patients according to their PK parameter values revealed two patient subgroups for each drug in which inter-patient variability was largely decreased compared to that in the total population.

Conclusions

This study provides a complete mathematical framework to optimize drug infusion pumps and inform on inter-patient PK variability, a step towards precise and personalized cancer chronotherapy.

Author summary

Accuracy and safety of infusion pumps remain a critical issue in the clinics and the development of accurate mathematical models to optimize drug administration though such devices has a key part to play in the advancement of precision medicine. Here, PK data from cancer patient receiving irinotecan, oxaliplatin and 5-fluorouracil into the hepatic artery via an infusion pump was mathematically investigated. A pump-to-patient model was designed and revealed significant inconsistencies between intended drug profiles and actual plasma concentrations. This mathematical model was then used to suggest improved profiles in order to minimise error and optimise delivery. Physiologically-based PK models of the three drugs were then linked to the pump-to-patient model. The whole framework achieved a very good fit to data and allowed quantifying inter-patient variability in PK parameters and linking them to potential clinical biomarkers via patient clustering. The developed methodology improves our understanding of patient-specific drug pharmacokinetics towards personalized drug administration.
Population codes of prior knowledge learned through environmental regularities
Authors: Quax Silvan C. , Bosch Sander E. , Peelen Marius V. , van Gerven Marcel A. J.
Published: July 2019

How the brain makes correct inferences about its environment based on noisy and ambiguous observations, is one of the fundamental questions in Neuroscience. Prior knowledge about the probability with which certain events occur in the environment plays an important role in this process. Humans are able to incorporate such prior knowledge in an efficient, Bayes optimal, way in many situations, but it remains an open question how the brain acquires and represents this prior knowledge. The long time spans over which prior knowledge is acquired make it a challenging question to investigate experimentally. In order to guide future experiments with clear empirical predictions, we used a neural network model to learn two commonly used tasks in the experimental literature (i.e. orientation classification and orientation estimation) where the prior probability of observing a certain stimulus is manipulated. We show that a population of neurons learns to correctly represent and incorporate prior knowledge, by only receiving feedback about the accuracy of their inference from trial-to-trial and without any probabilistic feedback. We identify different factors that can influence the neural responses to unexpected or expected stimuli, and find a novel mechanism that changes the activation threshold of neurons, depending on the prior probability of the encoded stimulus. In a task where estimating the exact stimulus value is important, more likely stimuli also led to denser tuning curve distributions and narrower tuning curves, allocating computational resources such that information processing is enhanced for more likely stimuli. These results can explain several different experimental findings and clarify why some contradicting observations concerning the neural responses to expected versus unexpected stimuli have been reported and pose some clear and testable predictions about the neural representation of prior knowledge that can guide future experiments.
A digital collection of rare and endangered lemurs and other primates from the Duke Lemur Center
Authors: Yapuncich Gabriel S. , Kemp Addison D. , Griffith Darbi M. , Gladman Justin T. , Ehmke Erin , Boyer Doug M.
Published: July 2019

Scientific study of lemurs, a group of primates found only on Madagascar, is crucial for understanding primate evolution. Unfortunately, lemurs are among the most endangered animals in the world, so there is a strong impetus to maximize as much scientific data as possible from available physical specimens. MicroCT scanning efforts at Duke University have resulted in scans of more than 100 strepsirrhine cadavers representing 18 species from the Duke Lemur Center. Scans include specimen overviews and focused, high-resolution selections of complex anatomical regions (e.g., cranium, hands, feet). Scans have been uploaded to MorphoSource, an online digital repository for 3D data. As captive (but free ranging) individuals, these specimens have a wealth of associated information that is largely unavailable for wild populations, including detailed life history data. This digital collection maximizes the information obtained from rare and endangered animals without degradation of the original specimens.
Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve
Authors: Kordy Kattayoun , Gaufin Thaidra , Mwangi Martin , Li Fan , Cerini Chiara , Lee David J. , Adisetiyo Helty , Woodward Cora , Pannaraj Pia S. , Tobin Nicole H. , Aldrovandi Grace M.
Published: July 2019

Increasing evidence supports the importance of the breast milk microbiome in seeding the infant gut. However, the origin of bacteria in milk and the process of milk microbe-mediated seeding of infant intestine need further elucidation. Presumed sources of bacteria in milk include locations of mother-infant and mother-environment interactions. We investigate the role of mother-infant interaction on breast milk microbes. Shotgun metagenomics and 16S rRNA gene sequencing identified milk microbes of mother-infant pairs in breastfed infants and in infants that have never latched. Although breast milk has low overall biomass, milk microbes play an important role in seeding the infant gut. Breast milk bacteria were largely comprised of Staphylococcus, Streptococcus, Acinetobacter, and Enterobacter primarily derived from maternal areolar skin and infant oral sites in breastfeeding pairs. This suggests that the process of breastfeeding is a potentially important mechanism for propagation of breast milk microbes through retrograde flux via infant oral and areolar skin contact. In one infant delivered via Caesarian section, a distinct strain of Bifidobacteria breve was identified in maternal rectum, breast milk and the infant’s stool potentially suggesting direct transmission. This may support the existence of microbial translocation of this anaerobic bacteria via the enteromammary pathway in humans, where maternal bacteria translocate across the maternal gut and are transferred to the mammary glands. Modulating sources of human milk microbiome seeding potentially imply opportunities to ultimately influence the development of the infant microbiome and health.
Injectable diblock copolypeptide hydrogel provides platform to maintain high local concentrations of taxol and local tumor control
Authors: Garrett Matthew C. , O’Shea Timothy M. , Wollenberg Alexander L. , Bernstein Alexander M. , Hung Derek , Staarman Brittany , Soto Horacio , Deming Timothy J. , Sofroniew Michael V. , Kornblum Harley I.
Published: July 2019

Introduction

Surgical resection and systemic chemotherapy with temozolomide remain the mainstay for treatment of glioblastoma. However, many patients are not candidates for surgical resection given inaccessible tumor location or poor health status. Furthermore, despite being first line treatment, temozolomide has only limited efficacy.

Methods

The development of injectable hydrogel-based carrier systems allows for the delivery of a wide range of chemotherapeutics that can achieve high local concentrations, thus potentially avoiding systemic side effects and wide-spread neurotoxicity. To test this modality in a realistic environment, we developed a diblock copolypeptide hydrogel (DCH) capable of carrying and releasing paclitaxel, a compound that we found to be highly potent against primary gliomasphere cells.

Results

The DCH produced minimal tissue reactivity and was well tolerated in the immune-competent mouse brain. Paclitaxel-loaded hydrogel induced less tissue damage, cellular inflammation and reactive astrocytes than cremaphor-taxol (typical taxol-carrier) or hydrogel alone. In a deep subcortical xenograft model, of glioblastoma in immunodeficient mice, injection of paclitaxel-loaded hydrogel led to a high local concentration of paclitaxel and led to local tumor control and improved survival. However, the tumor cells were highly migratory and were able to eventually escape the area of treatment.

Conclusions

These findings suggest this technology may be ultimately applicable to patients with deep-seated inoperable tumors, but as currently formulated, complete tumor eradication would be highly unlikely. Future studies should focus on targeting the migratory potential of surviving cells.
Effects of simulated acid rain on soil respiration rate and soil bacterial diversity in aPhyllostachyspubescensforest in subtropical China
Authors: Wang Nan , Pan Xiaocheng
Published: July 2019

Acid rain has been regarded as a global environmental concern due to its negative effects on global ecosystems. In this study, we investigated the effects of simulated acid rain (SAR) on soil respiration rate and soil bacterial diversity in a Moso bamboo (phyllostachyspubescens) forest in subtropical China. Experimental results showed a similar seasonal pattern of soil respiration rates underdifferent SAR treatments. Seasonal mean soil respiration rates for CK (control, deionized water, pH 6.7), T1 (pH 5.6), T2 (pH 4.0) and T3 (pH 2.5) treatments were 3.44, 4.80, 4.35 and 4.51 μ mol m−2s−1, respectively. One-way analysis of variance indicated that the SAR exposure had no significant effect on soil respiration (p>0.1) and soil microbial biomass (p>0.1). Soil bacterial community diversity was calculated as the Shannon-Wiener diversity index and the results showed that only T3 treatment had significant effects on soil bacterial diversity. The DGGE analysis results revealed that T1 and CK soils had closer association and were related to the T2 soil, while T3 soil was distinctly different from the other treatments. This work highlights that the effects of SAR are important to consider in assessing the soil respiration rate, particularly under the scenario of increasing acid rain pollution.
Effects of a novel thermophilic cellulose-degrading agent on the quality of compost and change in microbial community of garden waste
Authors: Fan Zhouzhou , Jia Zhenzhen , Li Yongshuang , Lian Peng , Peng Xiawei
Published: July 2019

Knowledge about the microbial communities in composting has advanced, but definitive knowledge concerning the application of actinomycetal communities in garden waste composting is still lacking. In this study, we compared the effects of amending compost with mixed agent M1 (five high-degradability strains) and other agents on the physicochemical indices and microbial community succession. The results showed that Pile A (only applying M1), exhibited a pH closer to neutral, the complete degradation of organic matter, and the highest remaining levels of nitrogen, phosphorus, and potassium. The seed germination rate, root length, and seed germination index values were significantly higher in piles amended with M1 and/or commercially available agents than in piles without exogenous microbial agents. Analyzing the microbial communities, these treatments were dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes during composting. The amount of Streptomyces was negatively correlated with the carbon/nitrogen ratio and positively correlated with total phosphorus and total potassium. Adding M1 increased microbial diversity, and the dominant microbial communities at the end of composting were similar to those found in the commercial microbial inoculum. Overall, agent M1 can shorten the composting process and increase the extent of degradation. This research provides additional insights into the potential function of Actinomycetes in compost ecology.
Serum miR-379 expression is related to the development and progression of hypercholesterolemia in non-alcoholic fatty liver disease
Authors: Okamoto Kinya , Koda Masahiko , Okamoto Toshiaki , Onoyama Takumi , Miyoshi Kenichi , Kishina Manabu , Matono Tomomitsu , Kato Jun , Tokunaga Shiho , Sugihara Takaaki , Hiramatsu Akira , Hyogo Hideyuki , Tobita Hiroshi , Sato Shuichi , Kawanaka Miwa , Hara Yuichi , Hino Keisuke , Chayama Kazuaki , Murawaki Yoshikazu , Isomoto Hajime
Published: July 2019

Introduction

Non-alcoholic fatty liver disease (NAFLD) has a wide spectrum, eventually leading to cirrhosis and hepatic carcinogenesis. We previously reported that a series of microRNAs (miRNAs) mapped in the 14q32.2 maternally imprinted gene region (Dlk1-Dio3 mat) are related to NAFLD development and progression in a mouse model. We examined the suitability of miR-379, a circulating Dlk1-Dio3 mat miRNA, as a human NAFLD biomarker.

Methods

Eighty NAFLD patients were recruited for this study. miR-379 was selected from the putative Dlk1-Dio3 mat miRNA cluster because it exhibited the greatest expression difference between NAFLD and non-alcoholic steatohepatitis in our preliminary study. Real-time PCR was used to examine the expression levels of miR-379 and miR-16 as an internal control.

Results

Compared to normal controls, serum miR-379 expression was significantly up-regulated in NAFLD patients. Receiver operating characteristic curve analysis suggested that miR-379 is a suitable marker for discriminating NAFLD patients from controls, with an area under the curve value of 0.72. Serum miR-379 exhibited positive correlations with alkaline phosphatase, total cholesterol, and low-density-lipoprotein cholesterol levels in patients with early stage NAFLD (Brunt fibrosis stage 0 to 1). The correlation between serum miR-379 and cholesterol levels was lost in early stage NAFLD patients treated with statins. Software-based predictions indicated that various energy metabolism–related genes, including insulin-like growth factor-1 (IGF-1) and IGF-1 receptor, are potential targets of miR-379.

Conclusions

Serum miR-379 exhibits high potential as a biomarker for NAFLD. miR-379 appears to increase cholesterol lipotoxicity, leading to the development and progression of NAFLD, via interference with the expression of target genes, including those related to the IGF-1 signaling pathway. Our results could facilitate future research into the pathogenesis, diagnosis, and treatment of NAFLD.
Dental Caries and Oral Health Behavior Assessment Among Portuguese Adolescents
Authors: Veiga Nélio Jorge , de Cecchi Maria Helena , Martins Johnny , da Cunha Inara Pereira , de Castro Meneghim Marcelo
Published: July 2019

Introduction

It is during the school phase that children and adolescents consolidate healthy behaviors, which will contribute to the decrease of diseases, especially in the reduction of dental caries. The main objective of the present study was to assess the decayed, missing and filled deciduous and permanent teeth index and oral health behaviors among Portuguese adolescents.

Materials and methods

An observational cross-sectional study was designed including a sample of 694 adolescents between the ages of 12 and 18 years old from five public schools in the Viseu and Guarda districts, Portugal. After a self-administered questionnaire was filled out by the participants, a clinical examination was carried out in order to assess oral status and dental caries identification. A descriptive analysis of the variables was performed using the Chi-square, Mann-Whitney and Kruskal-Wallis tests (p<0.05).

Results

The decayed, missing and filled permanent teeth index was 2.91±2.9 and the decayed, missing and filled deciduous teeth index was 1.10±1.4. Of the total sample, 73% consumed sugary food on a daily basis, 54.7% drank bottled water, 50.1% considered oral health good, 70.8% did not report pain in the last 12 months, but noticed gingival bleeding (51.5%). Most adolescents (79.4%) brushed their teeth daily and 60% did not use dental floss. Of the total sample, 96.4% had a dental appointment in the last 12 months, being 46.4% due to prevention treatments. The high decayed, missing and filled deciduous teeth index was associated with low maternal scholarship, male gender and living in a rural residence area (p<0.05). Adolescents who brush their teeth daily presented a good perception about their oral health (p<0.001).

Conclusions

Portuguese adolescents presented a low decayed, missing and filled deciduous and permanent teeth index index. The decayed, missing and filled deciduous teeth index was associated with sociodemographic factors. Oral hygiene habits were associated with self-perception of oral health. It is suggested that oral health promotion and prevention programs should be improved in schools in order to reduce the risks of oral disease development.
Dynamic healing and remodeling of mandibular ramus in segmental mobility and cortical overlap after intraoral vertical osteotomy
Authors: Lee Sang-Hwy , Cho Hoon , Kim Nam-Kyoo , Kim Bong Chul , Huh Jong-Ki , Yu Hyung Seog , Kim Hak-Jin
Published: July 2019

The ramus immediately after intraoral vertical ramus osteotomy (IVRO) shows segmental mobility, cortical overlap, and projection, which yield smooth-surfaced continuity and stability after one year. This study aimed to elucidate the three-dimensional (3D) morphological changes driven by regional healing and remodeling 12 months postoperatively (Post) and their relationships with the immediate postoperative (Imm) segmental overlapping pattern. We performed a retrospective study of the morphological change of mandibular ramus in terms of time and amount of cortical overlap after IVRO. 3D computed tomography data of 108 hemi-mandibles were analyzed by independent superimposition of Imm proximal and distal segment to Post mandible. Analysis showed extensive regional bone resorption and apposition resulting in a relatively flat-surfaced and morphologically intact Post ramus. The middle ramal remodeling was significantly associated with Imm overlapping patterns and Post mandibular movement, new bony projections of various shapes being observed at the posterior border of the Post ramus. The ramus after IVRO underwent dynamic morphological changes during healing/remodeling which were partly associated with Imm overlap. Moreover, the Post functional and smooth-surfaced ramus seems to have been facilitated by the close surgical approximation of segments and the postoperative mandibular functional rehabilitation, even with segmental positional changes.
Static Loading of the Knee Joint Results in Modified Single Leg Landing Biomechanics
Authors: Olson Michael W.
Published: July 2019

Background

External loading of the ligamentous tissues induces mechanical creep, which modifies neuromuscular response to perturbations. It is not well understood how ligamentous creep affects athletic performance and contributes to modifications of knee biomechanics during functional tasks.

Hypothesis/Purpose

The purpose of this study was to examine the mechanical and neuromuscular responses to single leg drop landing perturbations before and after passive loading of the knee joint.

Study Design

Descriptive laboratory study

Methods

Male (n=7) and female (n=14) participants’ (21.3 ± 2.1 yrs, 1.69 ± 0.09 m, 69.3 ± 13.0 kg) right hip, knee, and ankle kinematics were assessed during drop landings performed from a 30 cm height onto a force platform before and after a 10 min creep protocol. Electromyography (EMG) signals were recorded from rectus femoris (RF), vastus lateralis (VL), vastus medialis (VM), semimembranosus (SM), and biceps femoris (BF) muscles. The creep protocol involved fixing the knee joint at 35° during static loading with perpendicular loads of either 200 N (males) or 150 N (females). Maximum, minimum, range of motion (ROM), and angular velocities were assessed for the hip, knee, and ankle joints, while normalized average EMG (NAEMG), average vertical ground reaction forces (aVGRF), and rate of force development (RFD) were assessed at landing. Rate of force development (RFD) was calculated during the landings using ANOVAs. Alpha was set at 0.05.

Results

Maximum hip flexion velocity decreased (p < 0.01). Minimum knee flexion velocity increased (p < 0.02). Minimum knee ad/abduction velocity decreased (p < 0.001). Ankle ROM decreased (p < 0.001). aVGRF decreased (p < 0.02). RFD had a non-significant trend (p = 0.076). NAEMG was significant between muscle groups (p < 0.02).

Conclusion

Distinct changes in velocity parameters are attributed to the altered mechanical behavior of the knee joint tissues and may contribute to changes in the loading of the leg during landing.
Characterization of Sorbitol Dehydrogenase SmoS fromSinorhizobium meliloti1021
Authors: Kohlmeier MacLean G. , Bailey-Elkin Ben A. , Mark Brian L. , Oresnik Ivan J.
Published: July 2019

Sinorhizobium meliloti1021 is a Gram-negative alphaproteobacterium with a robust capacity for carbohydrate metabolism. The enzymes that facilitate these reactions assist in the survival of the bacterium across a range of environmental niches, and they may also be suitable for use in industrial processes. SmoS is a dehydrogenase that catalyzes the oxidation of the commonly occurring sugar alcohols sorbitol and galactitol into fructose and tagatose respectively using NAD+as a cofactor. The main objective of this study is to evaluate SmoS using biochemical techniques. The nucleotide sequence was codon optimized for heterologous expression inE. coliBL21 (DE3) GOLD cells, the protein was subsequently overexpressed and purified. Size exclusion chromatography and X-ray diffraction experiments suggest that SmoS is a tetrameric peptide. SmoS was crystallized to 2.1 Å in the absence of substrate and 2.0 Å in complex with sorbitol. SmoS was characterized kinetically and shown to have a preference for sorbitol despite a higher affinity for galactitol. Computational ligand docking experiments suggest that galactitol oxidation proceeds slowly because tagatose binds the protein in a more energetically favorable complex than fructose, and is retained in the active site for a longer time frame following oxidation which reduces the rate of the reaction. These results supplement the inventory of biomolecules with the potential for industrial applications and enhance our understanding of metabolism in the model organismS. meliloti.
The fitness landscape of the AfricanSalmonellaTyphimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Authors: Canals Rocío , Chaudhuri Roy R. , Steiner Rebecca E. , Owen Siân V. , Quinones-Olvera Natalia , Gordon Melita A. , Ibba Michael , Hinton Jay C. D.
Published: July 2019

We have used a transposon insertion sequencing (TIS) approach to establish the fitness landscape of the AfricanSalmonella entericaserovar Typhimurium ST313 strain D23580, to complement our previous comparative genomic and functional transcriptomic studies. We used a genome-wide transposon library with insertions every 10 nucleotides to identify genes required for survival and growthin vitroand during infection of murine macrophages. The analysis revealed genomic regions important for fitness under twoin vitrogrowth conditions. Overall, 724 coding genes were required for optimal growth in LB medium, and 851 coding genes were required for growth in SPI-2-inducing minimal medium. These findings were consistent with the essentiality analyses of otherS.Typhimurium ST19 and S. Typhi strains. The global mutagenesis approach also identified 60 sRNAs and 413 intergenic regions required for growth in at least onein vitrogrowth condition. By infecting murine macrophages with the transposon library, we identified 68 genes that were required for intra-macrophage replication but did not impact fitnessin vitro. None of these genes were unique toS.Typhimurium D23580, consistent with a high conservation of gene function betweenS.Typhimurium ST313 and ST19 and suggesting that novel virulence factors are not involved in the interaction of strain D23580 with murine macrophages. We discovered that transposon insertions rarely occurred in many pBT1 plasmid-encoded genes (36), compared with genes carried by the pSLT-BT virulence plasmid and other bacterial plasmids. The key essential protein encoded by pBT1 is a cysteinyl-tRNA synthetase, and our enzymological analysis revealed that the plasmid-encoded CysRSpBT1had a lower ability to charge tRNA than the chromosomally-encoded CysRSchrenzyme. The presence of aminoacyl-tRNA synthetases in plasmids from a range of gram-negative and gram-positive bacteria suggests that plasmid-encoded essential genes are more common than had been appreciated.
Detecting Gold-Labeled Cells
Authors: Rodig Scott J.
Published: July 2019

Colloidal gold particles bind tightly but not covalently to proteins at pH values that are around the protein's pI. Colloidal gold particles conjugated with a wide range of anti-immunoglobulin antibodies, Protein A, or streptavidin are available commercially. Gold labels were developed originally for electron microscopic studies, but they also work well at the level of the light microscope. They give higher resolution than enzyme-based methods and avoid the problems of substrate preparation and endogenous enzyme activity. Until recently, the gold labels lacked sensitivity at the level of light microscopy, but the recent development of the photochemical silver method of amplification, described here, has overcome this problem. Unamplified gold labels can be detected under the light microscope using bright-field illumination in which the label ranges from pale pink to deep red, depending on the strength of the reaction. Nomarski differential interference contrast microscopy makes the label appear dark red to black. With the silver enhancement method, the gold particles become coated in metallic silver and yield a black–brown label, best visualized by bright-field optics. Gold labeling methods are compatible with many histochemical stains. Gold labeling reactions are very readily controlled, because the appearance of staining can be monitored directly and continuously under the microscope.
Electroporation
Authors: Kumar Priti , Nagarajan Arvindhan , Uchil Pradeep D.
Published: July 2019

Electroporation is a process in which brief electrical pulses create transient pores in the plasma membrane that allow nucleic acids to enter the cellular cytoplasm. Here, we provide information on the history, mechanism, and optimization of electroporation. We also describe nucleofection, an improvement of the electroporation technology that permits the introduction of nucleic acids directly into the nucleus.