ResearchPad - spotlight https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Tracking the Genomic Footprints of SARS-CoV-2 Transmission]]> https://www.researchpad.co/article/elastic_article_13381 There is considerable public and scientific interest in the origin, spread, and evolution of SARS-CoV-2. Lu et al. recently conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains.

]]>
<![CDATA[Airway management for COVID-19: a move towards universal videolaryngoscope?]]> https://www.researchpad.co/article/N3d7075f6-4f30-4af5-8945-aae988bfe562 <![CDATA[Bread Feeding Is a Robust and More Physiological Enteropathogen Administration Method Compared to Oral Gavage]]> https://www.researchpad.co/article/N0d7618de-0124-4a3a-b8d0-5c0c86069bdf

Oral administration is a preferred model for studying infection by bacterial enteropathogens such as Yersinia spp. In the mouse model, the most frequent method for oral infection consists of oral gavage with a feeding needle directly introduced in the animal stomach via the esophagus. In this study, we compared needle gavage to bread feeding as an alternative mode of bacterial administration. Using bioluminescence-expressing strains of Yersinia pseudotuberculosis and Yersinia enterocolitica, we detected very early upon needle gavage a bioluminescent signal in the neck area together with a signal in the abdominal region, highlighting the presence of two independent sites of bacterial colonization and multiplication.

]]>
<![CDATA[Genetic Determinants of Altered Virulence of Type O Foot-and-Mouth Disease Virus]]> https://www.researchpad.co/article/N4b83c25a-7a72-4ca7-a0e7-a6fd11103b0d

FMD is probably the most important livestock disease in the world due to the severe economic consequences caused. The alteration of several viral genes may give the virus selective advantage to maintain its prevalence in nature. Here, we identified that a 70-nucleotide deletion in the S fragment combined with a single leucine insertion in the leader protein (Lpro) is a novel determinant of restricted growth on bovine cells, which significantly contributes to the altered virulence of serotype O FMDV in cattle. A synergistic and additive effect of the 70-nucleotide deletion in the S fragment and the single leucine insertion in Lpro on the virulence and host specificity of the virus was determined. These results will benefit efforts to understand the vial pathogenicity mechanism and molecular characteristics of FMDV.

]]>
<![CDATA[The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples]]> https://www.researchpad.co/article/N3787dd89-c57e-4551-922a-0fe584982752

The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.

]]>
<![CDATA[Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness]]> https://www.researchpad.co/article/N3593f6c2-a250-462f-aaa6-9485d6699926

Microbiologically influenced corrosion (MIC) is a complex process that generates economic losses to the industry every year. Corrosion must be managed to prevent a loss of containment of produced fluids to the external environment. MIC management includes the identification of assets with higher MIC risk, which could be influenced by nutrient levels in the system. Assessing biofilms under different nutrient conditions is essential for understanding the impact of flow regime on microbial communities and the subsequent impact on microbial corrosion and on the effectiveness of biocide treatment. This investigation simulates closely oil production systems, which contain piping sections exposed to continuous flow and sections that remain stagnant for long periods. Therefore, the results reported here are useful for MIC management and prevention. Moreover, the complementary methodological approach applied in this investigation highlighted the importance of implementing RNA-based methods for better identification of active microorganisms that survive stress conditions in oil systems.

]]>
<![CDATA[Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products]]> https://www.researchpad.co/article/N1f1cc765-09bd-43b3-8246-c40a5a4d104d

In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of “good bacteria” to protect food against spoilage organisms has a long, successful history, even though the molecular mechanisms are not fully understood. In this study, we show that the depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provide a link to the distinct, nonenzymatic, manganese-catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative Lactobacillus species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alternative to artificial preservation.

]]>
<![CDATA[Spastin joins LDs and peroxisomes in the interorganelle contact ballet]]> https://www.researchpad.co/article/N33b25519-6894-4a7e-9e8a-a9106810022b

W.M. Henne previews work from Chang et al. that demonstrates a role for Spastin in tethering lipid droplets to peroxisomes to facilitate fatty acid exchange.

]]>
<![CDATA[A precision RNA degradation machinery shapes stem cell development]]> https://www.researchpad.co/article/N7ad832cf-394f-43c3-ad12-9c59ba27baf4

Pereira and Arraiano preview work from the Wolin laboratory that uncovers an important regulatory role for the RNA exosome in stem cell development.

]]>
<![CDATA[Neurexin nanoclusters: A novel structure at presynaptic terminals]]> https://www.researchpad.co/article/Nb656b2c9-7bf0-4d6b-9e23-67da44a3db34

Kawaguchi and Gotoh highlight new work from Trotter et al. visualizing dynamic nanoclusters of neurexins in presynaptic terminals.

]]>
<![CDATA[Medium-Chain Fatty Acid Synthesis by “Candidatus Weimeria bifida” gen. nov., sp. nov., and “Candidatus Pseudoramibacter fermentans” sp. nov.]]> https://www.researchpad.co/article/N25b3a873-9825-4ef0-9457-636c89db8586

Chain elongation by medium-chain fatty acid (MCFA)-producing microbiomes offers an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain elongation are only beginning to be studied, and many of these organisms remain uncultured. We analyzed MCFA production by two uncultured organisms that were identified as the main MCFA producers in a microbial community enriched from an anaerobic digester; this characterization, which is based on meta-multi-omic analysis, complements the knowledge that has been acquired from pure-culture studies. The analysis revealed previously unreported features of the metabolism of MCFA-producing organisms.

]]>
<![CDATA[PAK Kinases Target Sortilin and Modulate Its Sorting]]> https://www.researchpad.co/article/Nc6f70eb3-9f6c-423a-a8f6-f09165a90327

The multifunctional type 1 receptor sortilin is involved in endocytosis and intracellular transport of ligands. The short intracellular domain of sortilin binds several cytoplasmic adaptor proteins (e.g., the AP-1 complex and GGA1 to -3), most of which target two well-defined motifs: a C-terminal acidic cluster dileucine motif and a YXXΦ motif in the proximal third of the domain. Both motifs contribute to endocytosis as well as Golgi-endosome trafficking of sortilin.

]]>
<![CDATA[MafB Is Important for Pancreatic β-Cell Maintenance under a MafA-Deficient Condition]]> https://www.researchpad.co/article/N3a8d8fc9-353a-46ea-a9b5-1a7a8dd874bb

The pancreatic-islet-enriched transcription factors MafA and MafB have unique expression patterns in β cells in rodents. MafA is specifically expressed in β cells and is a key regulatory factor for maintaining adult β-cell function, whereas MafB plays an essential role in β-cell development during embryogenesis, and its expression in β cells gradually decreases and is restricted to α cells after birth in rodents.

]]>
<![CDATA[Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1]]> https://www.researchpad.co/article/Nacf4d61c-7ec6-426b-a337-2916fc439c3c

Influenza A virus (IAV) is a respiratory pathogen of high importance to public health. Annual epidemics of seasonal IAV infections in humans are a significant public health and economic burden. IAV also causes sporadic pandemics, which can have devastating effects. The main target cells for IAV replication are epithelial cells in the respiratory epithelium. The cellular innate immune responses induced in these cells upon infection are critical for defense against the virus, and therefore, it is important to understand the complex interactions between the virus and the host cells. In this study, we investigated the innate immune response to IAV in the respiratory epithelium at the single-cell level, providing a better understanding on how a population of epithelial cells functions as a complex system to orchestrate the response to virus infection and how the virus counteracts this system.

]]>
<![CDATA[TRIM69 Inhibits Vesicular Stomatitis Indiana Virus]]> https://www.researchpad.co/article/Naf57ddcc-d43f-449c-af81-730cdb8d19b1

Vesicular stomatitis Indiana virus (VSIV) is a veterinary pathogen that is also used as a backbone for many oncolytic and vaccine strategies. In natural and therapeutic settings, viral infections like VSIV are sensed by the host, and as a result the host cells make proteins that can protect them from viruses. In the case of VSIV, these antiviral proteins constrain viral replication and protect most healthy tissues from virus infection. In order to understand how VSIV causes disease and how healthy tissues are protected from VSIV-based therapies, it is crucial that we identify the proteins that inhibit VSIV. Here, we show that TRIM69 is an antiviral defense that can potently and specifically block VSIV infection.

]]>
<![CDATA[Crystal Structure of the Catalytic and Cytochrome b Domains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase]]> https://www.researchpad.co/article/Ne30e25a1-dc05-4c60-b592-bae583841ee9

Pyrroloquinoline quinone (PQQ) is known as the “third coenzyme” following nicotinamide and flavin. PQQ-dependent enzymes have previously been found only in prokaryotes, and the existence of a eukaryotic PQQ-dependent enzyme was in doubt. In 2014, we found an enzyme in mushrooms that catalyzes the oxidation of various sugars in a PQQ-dependent manner and that was a PQQ-dependent enzyme found in eukaryotes. This paper presents the X-ray crystal structures of this eukaryotic PQQ-dependent quinohemoprotein, which show the active site, and identifies the amino acid residues involved in the binding of the cofactor PQQ. The presented X-ray structures reveal that the AA12 domain is in a binary complex with the coenzyme, clearly proving that PQQ-dependent enzymes exist in eukaryotes as well as prokaryotes. Because no biosynthetic system for PQQ has been reported in eukaryotes, future research on the symbiotic systems is expected.

]]>
<![CDATA[Building perception block by block: a response to Fekete et al.]]> https://www.researchpad.co/article/5c6861b5d5eed0c484021f16

Abstract

Is consciousness a continuous stream, or do percepts occur only at certain moments of time? This age-old question is still under debate. Both positions face difficult problems, which we proposed to overcome with a 2-stage model, where unconscious processing continuously integrates information before a discrete, conscious percept occurs. Recently, Fekete et al. criticized our model. Here, we show that, contrary to their proposal, simple sliding windows cannot explain apparent motion and related phenomena within a continuous framework, and that their supervenience argument only holds true for qualia realists, a philosophical position we do not adopt.

]]>
<![CDATA[Measuring states of pathological (un)consciousness: research dimensions, clinical applications, and ethics†]]> https://www.researchpad.co/article/5c081857d5eed0c484f447dc

Abstract

Consciousness is a multidimensional construct with no widely accepted definition. Especially in pathological conditions, it is less clear what exactly is meant by (un)consciousness, how it can be reliably observed or measured. Here, we aim at (i) bringing together state of the art approaches to classification of single patients suffering from disorders of consciousness by means of motor-independent assessment of consciousness states with electrophysiology and functional neuroimaging, (ii) showing how each proposed metric translates into clinical practice and (iii) raising a discussion on the ethical aspects of consciousness measurements. We realize that when dealing with patients some issues commonly pertain to each methodology discussed here, such as the overall clinical condition, clinical heterogeneity, and diagnostic uncertainty. When predicting patients’ diagnosis, though, each method adopts a different approach to determine (a) a “gold standard” of the benchmark population upon which the metric is computed and (b) the generalization and replicability in the attempt to avoid overfitting. From an applied ethics perspective, the focus is, hence, on knowing what one is measuring and on the validity of measurements. We conclude that, when searching for consciousness in pathological conditions, confident diagnosis can be based on the use of probabilistic predictions as well as on accumulative evidence stemming from multiple non-overlapping assessments with different modalities. A framework which will regulate the application order of these techniques (balancing their availability, sensitivity, and specificity, based on underlying clinical assumptions about a patient’s conscious state), is expected to ameliorate clinical management and further inform on the critical patterns of (un)consciousness.

]]>
<![CDATA[Are we underestimating the richness of visual experience?]]> https://www.researchpad.co/article/5c081853d5eed0c484f44757

Abstract

It has been argued that the bandwidth of perceptual experience is low—that the richness of experience is illusory and that the amount of visual information observers can perceive and remember is extremely limited. However, the evidence suggests that this postulated poverty of experiential content is illusory and that visual phenomenology is immensely rich. To properly estimate perceptual content, experimentalists must move beyond the limitations of binary alternative-forced choice procedures and analyze reports of experience more broadly. This will open our eyes to the true richness of experience and to its neuronal substrates.

]]>
<![CDATA[Measuring away an attentional confound?]]> https://www.researchpad.co/article/5c08186ad5eed0c484f44b60

Abstract

A recent fMRI study by Webb et al. (Cortical networks involved in visual awareness independent of visual attention, Proc Natl Acad Sci U S A 2016;113:13923–28) proposes a new method for finding the neural correlates of awareness by matching attention across awareness conditions. The experimental design, however, seems at odds with known features of attention. We highlight logical and methodological points that are critical when trying to disentangle attention and awareness.

]]>