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Pathogens are among the most limiting factors for crop success and expansion. Thus, finding the underlying genetic cause of pathogen resistance is the main goal for plant geneticists. The activation of a plant’s immune system is mediated by the presence of specific receptors known as disease-resistance genes (R genes). Typical R genes encode functional immune receptors with nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) domains, making the NBS-LRRs the largest family of plant resistance genes. Establishing host resistance is crucial for plant growth and crop yield but also for reducing pesticide use. In this regard, pyramiding R genes is thought to be the most ecologically friendly way to enhance the durability of resistance. To accomplish this, researchers must first identify the related genes, or linked markers, within the genomes. However, the duplicated nature, with the presence of frequent paralogues, and clustered characteristic of NLRs make them difficult to predict with the classic automatic gene annotation pipelines. In the last several years, efforts have been made to develop new methods leading to a proliferation of reports on cloned genes. Herein, we review the bioinformatic tools to assist the discovery of R genes in plants, focusing on well-established pipelines with an important computer-based component.

Biowastes can enhance the establishment of New Zealand (NZ) native vegetation, particularly on degraded land, where biological or physicochemical deficiencies limit plant growth. We identified critical success factors influencing selection and use of biowastes for a) growing native plants and b) rehabilitating native ecosystems. These were: weed competition; resilience (especially to drought and storms); ecosystem succession; and soil microbiome responses to elevated Nitrogen, Phosphorus, Organic Matter (OM) and contaminants (including Trace Elements). These factors determine the selection, timing and methods of biowaste application, selection of plant species and target ecosystems, and post-application management of receiving sites. Commonly planted native NZ species benefit from biowastes application where soils have depleted OM or sites with surface crusting, erosion, or high exposure to wind and temperature fluctuations. Commonly planted native species display luxury uptake of macro-nutrients, even on soils that are low-fertility under agricultural standards. Therefore, the growth responses to additional nutrients may be small. In contrast, most exotic weeds outcompete NZ species in high fertility soils. Therefore, biowaste application should not result in excessive nutrient availability. This can be achieved by using blends that contain a high-carbon biowaste, such as wood-waste, which immobilizes some macronutrients in the short term. We recommend long-term research using mixed-species field trials to identify biowastes and application methods that together support development of resilient native ecosystems. In particular, research should determine the role of biowastes on the beneficial mycorrhizae and native soil fauna. Application methods that enhance heterogeneity may help retain and/or build responsive microbiomes while conserving “native” microbiomes to deliver sustainable, rehabilitated native ecosystems.

Adaptation is a key component of efficient coding in sensory neurons. However, it remains unclear how neurons can provide a stable representation of external stimuli given their history-dependent responses. Here we show that a stable representation is maintained if efficiency is optimized by a population of neurons rather than by neurons individually. We show that spike-frequency adaptation and E/I balanced recurrent connectivity emerge as solutions to a global cost-accuracy tradeoff. The network will redistribute sensory responses from highly excitable neurons to less excitable neurons as the cost of neural activity increases. This does not change the representation at the population level despite causing dynamic changes in individual neurons. By applying this framework to an orientation coding network, we reconcile neural and behavioral findings. Our approach underscores the common mechanisms behind the diversity of neural adaptation and its role in producing a reliable representation of the stimulus while minimizing metabolic cost.

Background. Rheumatoid arthritis (RA) is a systemic autoimmune disease associated with immune dysregulation and increased risk of infections. The presence of autoantibodies and immunoglobulin abnormalities indicates B-cell and antibody-secreting cell (ASC) dysfunction. We hypothesize that soluble factors associated with B-cell and ASC activity are decreased in RA patients and that this is linked to higher susceptibility to infections. Methods. Using the Johns Hopkins Arthritis Cohort and Biorepository, we contrasted serum protein levels of soluble factors involved in B-cell activation (CD40, CD40L) and B-cell/ASC homing (CXCL10, CXCL11, and CXCL13) or survival (BAFF, APRIL, TACI, and BCMA) in 10 healthy subjects and 23 adult RA patients (aged 24-65 years). We subdivided RA patients into those with (n=17) and those without infections (n=6) within a 2-year period. In order to reduce the effect of RA treatment, we only included patients receiving methotrexate monotherapy or no RA treatments at baseline. Soluble serum protein levels of B-cell/ASC factors were quantified by multiplex immunoassays. Results. We identified that (1) serum levels of soluble BCMA, APRIL, CD40, and CD40L were significantly decreased in RA patients relative to healthy individuals; (2) serum soluble BCMA, predominantly released by ASC, correlated with serum concentrations of class-switched immunoglobulins, IgG and IgA; and (3) RA patients with a history of infections had significantly lower soluble BCMA levels compared with healthy donors and with RA patients without infections. Conclusions. Our study using soluble factors linked to B-cell/ASC activation and survival suggests that there is a paucity of ASC in a subset of RA patients and that this may be linked to altered antibody production and increased risk of infections. Further delineating the link between ASC and infection susceptibility in RA may optimize disease management and provide novel insights into disease pathogenesis that are susceptible to intervention.

Firewalls, especially at large organizations, process high velocity internet traffic and flag suspicious events and activities. Flagged events can be benign, such as misconfigured routers, or malignant, such as a hacker trying to gain access to a specific computer. Confounding this is that flagged events are not always obvious in their danger and the high velocity nature of the problem. Current work in firewall log analysis is manual intensive and involves manpower hours to find events to investigate. This is predominantly achieved by manually sorting firewall and intrusion detection/prevention system log data. This work aims to improve the ability of analysts to find events for cyber forensics analysis. A tabulated vector approach is proposed to create meaningful state vectors from time-oriented blocks. Multivariate and graphical analysis is then used to analyze state vectors in human–machine collaborative interface. Statistical tools, such as the Mahalanobis distance, factor analysis, and histogram matrices, are employed for outlier detection. This research also introduces the breakdown distance heuristic as a decomposition of the Mahalanobis distance, by indicating which variables contributed most to its value. This work further explores the application of the tabulated vector approach methodology on collected firewall logs. Lastly, the analytic methodologies employed are integrated into embedded analytic tools so that cyber analysts on the front-line can efficiently deploy the anomaly detection capabilities.

Over the past two decades, several studies have positioned early-life microbial exposure as a key factor for protection or susceptibility to respiratory diseases. Birth cohorts have identified a strong link between neonatal bacterial colonization of the nasal airway and gut with the risk for respiratory infections and childhood asthma. Translational studies have provided companion mechanistic insights on how viral and bacterial exposures in early life affect immune development at the respiratory mucosal barrier. In this review, we summarize and discuss our current understanding of how early microbial–immune interactions occur during infancy, with a particular focus on the emergent paradigm of “innate immune training”. Future human-based studies including newborns and infants are needed to inform the timing and key pathways implicated in the development, maturation, and innate training of the airway immune response, and how early microbiota and virus exposures modulate these processes in the respiratory system during health and disease.

Lung cancer is one of the most frequently diagnosed cancers accounting for the highest number of cancer-related deaths in the world. Despite significant progress including targeted therapies and immunotherapy, the treatment of advanced lung cancer remains challenging. Targeted therapies are highly efficacious at prolonging life, but not curative. In prior work we have identified Ubiquitin Specific Protease 13 (USP13) as a potential target to significantly enhance the efficacy of mutant EGFR inhibition. The current study aimed to develop lead molecules for the treatment of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) by developing potent USP13 inhibitors initially starting from Spautin-1, the only available USP13 inhibitor. A SAR study was performed which revealed that increasing the chain length between the secondary amine and phenyl group and introducing a halogen capable of inducing a halogen bond at position 4’ of the phenyl group, dramatically increased the activity. However, we could not confirm the binding between Spautin-1 (or its analogues) and USP13 using isothermal titration calorimetry (ITC) or thermal shift assay (TSA) but do not exclude binding under physiological conditions. Nevertheless, we found that the anti-proliferative activity displayed by Spautin-1 towards EGFR-mutant NSCLC cells in vitro was at least partially associated with kinase inhibition. In this work, we present N-[2-(substituted-phenyl)ethyl]-6-fluoro-4-quinazolinamines as promising lead compounds for the treatment of NSCLC. These analogues are significantly more effective towards EGFR-mutant NSCLC cells than Spautin-1 and act as potent never in mitosis A related kinase 4 (NEK4) inhibitors (IC50~1 µM) with moderate selectivity over other kinases.

Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.

Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member of a highly conserved family of RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21–22 nucleotides in length. Zinc finger nucleases (ZFNs) were used to generate single and double-mutants of putative soybean DCL1 homologs, DCL1a and DCL1b, to confirm their functional role(s) in the soybean miRNA pathway. Neither DCL1 single mutant, dcl1a or dcl1b plants, exhibited a pronounced morphological or molecular phenotype. However, the dcl1a/dcl1b double mutant expressed a strong morphological phenotype, characterized by reduced seed size and aborted seedling development, in addition to defective miRNA precursor transcript processing efficiency and deregulated miRNA target gene expression. Together, these findings indicate that the two soybean DCL1 paralogs, DCL1a and DCL1b, largely play functionally redundant roles in the miRNA pathway and are essential for normal plant development.

DNA methylation (DNAm) is an essential mechanism governing normal development in humans. Although most DNAm patterns in blood cells are established in utero, the genes associated with immune function undergo postnatal DNAm modifications, and the characterization of this subset of genes is incomplete. Accordingly, we used available longitudinal DNAm datasets from a large birth cohort in the U.S. to further identify postnatal DNAm variation in peripheral leukocytes from 105 children (n = 105) between birth and the first two years of life, as determined by postnatal changes in β values (with the percentage of methylation ranging from 0 to 1.0 at individual CpG sites). Our study is an extension of a previous analysis performed by our group and identified that: (1) as previously described, DNAm patterns at most CpG sites were established before birth and only a small group of genes underwent DNAm modifications postnatally, (2) this subset includes multiple immune genes critical for lymphocyte development, and (3) several members of the tumor necrosis factor receptor and cytokine superfamilies with essential roles in immune cell activation, survival, and lymphoid tissue development were among those with a larger postnatal variation. This study describes the precise epigenetic DNA methylation marks in important immune genes that change postnatally and raises relevant questions about the role of DNAm during postnatal immune development in early childhood.

Neurodegenerative diseases in which the decrease of the acetylcholine is observed are growing worldwide. In the present study, a series of new arylaminopropanone derivatives with N-phenylcarbamate moiety (1–16) were prepared as potential acetylcholinesterase and butyrylcholinesterase inhibitors. In vitro enzyme assays were performed; the results are expressed as a percentage of inhibition and the IC50 values. The inhibitory activities were compared with reference drugs galantamine and rivastigmine showing piperidine derivatives (1–3) as the most potent. A possible mechanism of action for these compounds was determined from a molecular modelling study by using combined techniques of docking, molecular dynamics simulations and quantum mechanics calculations.

Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectroscopy (MALDI-TOF MS) has been used routinely over the past decade in clinical microbiology laboratories to rapidly characterize diverse microorganisms of medical importance both at the genus and species levels. Currently, there is keen interest in applying MALDI-TOF MS at taxonomic levels beyond species and to characterize environmental isolates. We constructed a model system consisting of 19 isolates of Deinococcus aquaticus obtained from biofilm communities indigenous to diverse substrates (concrete, leaf tissue, metal, and wood) in the Fox River – Lake Winnebago system of Wisconsin to: (1) develop rapid sample preparation methods that produce high quality, reproducible MALDI-TOF spectra and (2) compare the performance of MALDI-TOF MS-based profiling to common DNA-based approaches including 16S rRNA sequencing and genomic diversity by BOX-A1R fingerprinting. Our results suggest that MALDI-TOF MS can be used to rapidly and reproducibly characterize environmental isolates of D. aquaticus at the subpopulation level. MALDI-TOF MS provided higher taxonomic resolution than either 16S rRNA gene sequence analysis or BOX-A1R fingerprinting. Spectra contained features that appeared to permit characterization of isolates into two co-occurring subpopulations. However, reliable strain-level performance required rigorous and systematic standardization of culture conditions and sample preparation. Our work suggests that MALDI-TOF MS offers promise as a rapid, reproducible, and high-resolution approach to characterize environmental isolates of members of the genus Deinococcus. Future work will focus upon application of methods described here to additional members of this ecologically diverse and ubiquitous genus.

The objective of this study is to describe the clinical features and computed tomography (CT) findings of dogs with retrobulbar disease. There are two facets to this study: a retrospective case series in which findings of dogs with primary vs. secondary retrobulbar disease are described, and a retrospective cross-sectional study in which computed tomography findings of dogs with retrobulbar neoplasia vs. infection/inflammation are described and compared. The medical records of 66 client-owned dogs diagnosed with retrobulbar disease between 2006 and 2016 were reviewed. Clinical information including signalment, the specialty service to which the dog was presented, clinical signs, physical examination findings, diagnostic results, treatment, and outcome were documented. Diagnostic imaging and histopathology were reviewed. Forty-one dogs (62.1%) were diagnosed with primary disease of the retrobulbar space; 25 dogs (37.9%) were considered to have secondary retrobulbar disease. Of the 41 dogs with primary retrobulbar disease, 19 were diagnosed with neoplasia, 19 with infectious/inflammatory disease, and 3 suffered traumatic insult to the retrobulbar space. Of the 25 dogs with secondary retrobulbar disease, 21 were diagnosed with neoplasia, 3 with infectious/inflammatory disease, and 1 with a cyst. Dogs had a combination of ocular, oral, and/or nasal clinical signs. CT findings of orbital osteolysis, orbital periosteal reaction, and presence of a retrobulbar mass were significantly associated with neoplasia, while zygomatic salivary gland enlargement, retrobulbar mass effect, and mandibular lymphadenopathy were more often associated with infectious/inflammatory disease. CT findings overlap among different retrobulbar diseases, but new bone formation and lysis are more often associated with neoplasia. Disease originating from the retrobulbar space was equally likely to be infectious/inflammatory (n = 19) or neoplastic (n = 19), based on definitive diagnostic results of dogs with primary retrobulbar disease. Due to the clinical ramifications of these disorders, the diagnosis and treatment of these cases should be managed with a multi-specialty approach.

Healthcare-acquired infections (HAI) have a significant influence in the morbidity and mortality in hospitals. Traditionally, the prevention of the HAI involves two strategies: the use of inert materials, including stainless steel for furniture and equipment, and the disinfection of devices and facilities. In this work, we evaluate a self- assembled polymer layer with silver nanoparticles as an alternative coating on mild carbon steel for the substitution of the more expensive stainless steel and the traditional disinfection procedures. We evaluated the electrochemical response of five different compounds for the self-assembled monolayer (SAM): adipic acid (AA), cysteine (CYS), glycine (GLY), polyethylene glycol (PEG) and polyethylenimine (PEI). The electrochemical stability of the coated steel was evaluated by open circuit potential measurement (OCP), electrochemical impedance spectroscopy (EIS) and linear sweep voltammetry (LSV). For the physicochemical evaluation we used Fourier transform infrared (FTIR), Ultraviolet-visible (UV) spectroscopy and dynamic light scattering (DLS). Then, according to the results we selected the SAMs obtained with adipic acid and glycine to test their assembly with Ag nanoparticles. These coatings were evaluated by electrochemical and microbiological test. The microbiological evaluation of the silver nanoparticles inhibitory effect was performed through a modified microdilution method using Candidas spp. The results showed a relationship between the self-assembled layer synthesis procedures and the expected functions that are a low minimal inhibitory concentration (MIC) and the prevention of the corrosion of the mild carbon steel.

Sin resumen

Sin resumen

Sin resumen

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that emerged in 2012, causing severe pneumonia and acute respiratory distress syndrome (ARDS), with a case fatality rate of ~36%. When expressed in isolation, CoV accessory proteins have been shown to interfere with innate antiviral signaling pathways. However, there is limited information on the specific contribution of MERS-CoV accessory protein 4b to the repression of the innate antiviral response in the context of infection. We found that MERS-CoV 4b was required to prevent a robust NF-κB dependent response during infection. In wild-type virus infected cells, 4b localized to the nucleus, while NF-κB was retained in the cytoplasm. In contrast, in the absence of 4b or in the presence of cytoplasmic 4b mutants lacking a nuclear localization signal (NLS), NF-κB was translocated to the nucleus leading to the expression of pro-inflammatory cytokines. This indicates that NF-κB repression required the nuclear import of 4b mediated by a specific NLS. Interestingly, we also found that both in isolation and during infection, 4b interacted with α-karyopherin proteins in an NLS-dependent manner. In particular, 4b had a strong preference for binding karyopherin-α4 (KPNA4), which is known to translocate the NF-κB protein complex into the nucleus. Binding of 4b to KPNA4 during infection inhibited its interaction with NF-κB-p65 subunit. Thereby we propose a model where 4b outcompetes NF-κB for KPNA4 binding and translocation into the nucleus as a mechanism of interference with the NF-κB-mediated innate immune response.