On the covalent nature of lysine polyphosphorylation.

Post-translational modifications of proteins (PTMs) introduce an extra layer of complexity to cellular regulation. Although phosphorylation of serine, threonine, and tyrosine residues is well-known as PTMs, lysine is, in fact, the most heavily modified amino acid, with over 30 types of PTMs on lysine having been characterized. One of the most recently discovered PTMs on lysine residues is polyphosphorylation, which sees linear chains of inorganic polyphosphates (polyP) attached to lysine residues. The labile nature of phosphoramidate bonds raises the question of whether this modification is covalent in nature. Here, we used buffers with very high ionic strength, which would disrupt any non-covalent interactions, and confirmed that lysine polyphosphorylation occurs covalently on proteins containing PASK domains (polyacidic, serine-, and lysine-rich), such as the budding yeast protein nuclear signal recognition 1 (Nsr1) and the mammalian protein nucleolin. This Matters Arising Response paper addresses the Neville et al. (2024) Matters Arising paper, published concurrently in Molecular Cell.

Polyphosphate attachment to lysine repeats is a non-covalent protein modification.

Polyphosphate (polyP) is a chain of inorganic phosphate that is present in all domains of life and affects diverse cellular phenomena, ranging from blood clotting to cancer. A study by Azevedo et al. described a protein modification whereby polyP is attached to lysine residues within polyacidic serine and lysine (PASK) motifs via what the authors claimed to be covalent phosphoramidate bonding. This was based largely on the remarkable ability of the modification to survive extreme denaturing conditions. Our study demonstrates that lysine polyphosphorylation is non-covalent, based on its sensitivity to ionic strength and lysine protonation and absence of phosphoramidate bond formation, as analyzed via 31P NMR. Ionic interaction with lysine residues alone is sufficient for polyP modification, and we present a new list of non-PASK lysine repeat proteins that undergo polyP modification. This work clarifies the biochemistry of polyP-lysine modification, with important implications for both studying and modulating this phenomenon. This Matters Arising paper is in response to Azevedo et al. (2015), published in Molecular Cell. See also the Matters Arising Response by Azevedo et al. (2024), published in this issue.

Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions.

Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively upregulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning, and memory deficits, accompanied by altered hippocampal synaptic plasticity. We provide evidence that the eIF4G microexons function as a translational brake by causing ribosome stalling, through their propensity to promote the coalescence of cytoplasmic granule components associated with translation repression, including the fragile X mental retardation protein FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes neuronal translation to control higher order cognitive functioning.

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons.

Alternative splicing is crucial for diverse cellular, developmental, and pathological processes. However, the full networks of factors that control individual splicing events are not known. Here, we describe a CRISPR-based strategy for the genome-wide elucidation of pathways that control splicing and apply it to microexons with important functions in nervous system development and that are commonly misregulated in autism. Approximately 200 genes associated with functionally diverse regulatory layers and enriched in genetic links to autism control neuronal microexons. Remarkably, the widely expressed RNA binding proteins Srsf11 and Rnps1 directly, preferentially, and frequently co-activate these microexons. These factors form critical interactions with the neuronal splicing regulator Srrm4 and a bi-partite intronic splicing enhancer element to promote spliceosome formation. Our study thus presents a versatile system for the identification of entire splicing regulatory pathways and further reveals a common mechanism for the definition of neuronal microexons that is disrupted in autism.

Isolated non-immune mediated second-degree atrioventricular block in fetus: natural history and predictive factors for spontaneous recovery.

OBJECTIVES: To uncover the clinical course of fetal isolated non-immune mediated second-degree AVB and determine the factors associated with the spontaneous recovery for fetal non-immune second-degree atrioventricular block (AVB). METHODS: A total of 20 fetuses with isolated, non-immune mediated second-degree AVB were prospectively recruited between 2014 and 2022. These fetuses were divided into the spontaneous recovery group (n=12) and the non-spontaneous recovery group (n=8). Maternal and fetal basic characteristics, intrauterine and postnatal outcomes were compared between groups. RESULTS: Twelve fetuses restored 1:1 atrioventricular conduction in utero and did not recur during the postnatal follow-up period. The residual eight fetuses maintained as second-degree AVB and six of them were aborted due to parental request in utero. Of the two live children with second-degree AVB, one of them progressed to complete AVB at the latest follow up at the age of 34 months, but without any symptoms, heart enlargement or dysfunction. The residual one progressed to complete AVB and was finally diagnosed with type 2 long-QT syndrome. Fetuses in the spontaneous recovery group presented with earlier gestational age at diagnosis (20.0[17.0-26.0] vs. 24.5[18.0-35.0] weeks, p=0.004) and higher atrial rate (147[130-160] vs 138.00[125.00-149.00] bpm, p=0.006) in comparison with the non-spontaneous recovery group. A cut-off value of 22.5 weeks of gestational age and 144 bpm of atrial rate at diagnosis could predict the failure of spontaneous recovery, with sensitivities of 87.5%, 75%, and specificities of 92.0%, 87.5%, respectively. CONCLUSIONS: The outcome of fetal non-immune second-degree AVB was favorable. Earlier gestational age at diagnosis and higher atrial rate were related to spontaneous reversion for isolated non-immune-mediated second-degree AVB. However, prenatal gene test should be performed for those with persistent AVB to exclude the heritable disorders including LQTS. These findings may provide important references for clinical management and prenatal counseling. This article is protected by copyright. All rights reserved.

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders.

A key challenge in understanding and ultimately treating autism is to identify common molecular mechanisms underlying this genetically heterogeneous disorder. Transcriptomic profiling of autistic brains has revealed correlated misregulation of the neuronal splicing regulator nSR100/SRRM4 and its target microexon splicing program in more than one-third of analyzed individuals. To investigate whether nSR100 misregulation is causally linked to autism, we generated mutant mice with reduced levels of this protein and its target splicing program. Remarkably, these mice display multiple autistic-like features, including altered social behaviors, synaptic density, and signaling. Moreover, increased neuronal activity, which is often associated with autism, results in a rapid decrease in nSR100 and splicing of microexons that significantly overlap those misregulated in autistic brains. Collectively, our results provide evidence that misregulation of an nSR100-dependent splicing network controlled by changes in neuronal activity is causally linked to a substantial fraction of autism cases.

A Bioengineered Nisin Derivative To Control Streptococcus uberis Biofilms.

Antimicrobial peptides are evolving as novel therapeutic options against the increasing problem of multidrug-resistant microorganisms, and nisin is one such avenue. However, some bacteria possess a specific nisin resistance system (NSR), which cleaves the peptide reducing its bactericidal efficacy. NSR-based resistance was identified in strains of Streptococcus uberis, a ubiquitous pathogen that causes mastitis in dairy cattle. Previous studies have demonstrated that a nisin A derivative termed nisin PV, featuring S29P and I30V, exhibits enhanced resistance to proteolytic cleavage by NSR. Our objective was to investigate the ability of this nisin derivative to eradicate and inhibit biofilms of S. uberis DPC 5344 and S. uberis ATCC 700407 (nsr+) using crystal violet (biomass), 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) (viability) assays, and confocal microscopy (viability and architecture). When preestablished biofilms were assessed, both peptides reduced biofilm biomass by over 60% compared to that of the untreated controls. However, a 42% higher reduction in viability was observed following treatment with nisin PV compared to that of nisin A. Accordingly, confocal microscopy analysis revealed significantly more dead cells on the biofilm upper surface and a reduced thickness following treatment with nisin PV. When biofilm inhibition was assessed, nisin PV inhibited biofilm formation and decreased viability up to 56% and 85% more than nisin A, respectively. Confocal microscopy analysis revealed a lack of biofilm for S. uberis ATCC 700407 and only dead cells for S. uberis DPC 5344. These results suggest that nisin PV is a promising alternative to effectively reduce the biofilm formation of S. uberis strains carrying NSR. IMPORTANCE One of the four most prevalent species of bovine mastitis-causing pathogens is S. uberis. Its ability to form biofilms confers on the bacteria greater resistance to antibiotics, requiring higher doses to be more effective. In a bid to limit antibiotic resistance development, the need for alternative antimicrobials is paramount. Bacteriocins such as nisin represent one such alternative that could alleviate the impact of mastitis caused by S. uberis. However, many strains of S. uberis have been shown to possess nisin resistance determinants, such as the nisin resistance protein (NSR). In this study, we demonstrate the ability of nisin and a nisin derivative termed PV that is insensitive to NSR to prevent and remove biofilms of NSR-producing S. uberis strains. These findings will add new information to the antimicrobial bacteriocins and control of S. uberis research fields specifically in relation to biofilms and nsr+ mastitis-associated strains.

Trends in United States neurosurgery residency education and training over the last decade (2009-2019).

OBJECTIVE: Postgraduate training in medicine has been under scrutiny in the last 10 years, with a focus on improving residents' education. The aim of this study was to quantify trends in neurosurgery residency (NSR) training and education over the last 10 years. METHODS: The authors assessed Accreditation Council for Graduate Medical Education (ACGME), National Resident Matching Program, and American Board of Neurological Surgeons records and searched PubMed to collate 2009-2019 data. Analyzed trends included residents' demographic data, programs' characteristics, graduation and attrition rates, match data, resident case logs, and qualitative educational curriculum changes. RESULTS: Significant increases in residents' demographic data (p < 0.05) included the number of female residents (from 12.7% to 17.6%) and the absolute number of residents (from 1112 to 1462). Age (mean 28.8 years), ethnicity, and number of residents per program (mean 13 residents per program) were unchanged. There were 16 new ACGME NSR programs, with currently 115 programs nationwide. The number of applicants per year (324 applicants per year) and the matching rate (mean 64%) remained stable. The mean attrition rate of 2.6% (range 2%-4%) was higher than the mean 2.1% ACGME attrition rate, a rate that decreased from 3% in 2009 to 1.6% in 2019. Education curriculum changes aimed at the standardization of training across the US included residents' boot camp (2009), the Milestones project (2012), and mandatory 7-year training initiated in 2013. An increase in endovascular, functional, trauma, and spine resident caseload was noted. The number of yearly publications about US NSR education has significantly increased (p < 0.05). CONCLUSIONS: NSR education has received greater attention over the last decade in the US. Standardization of training has been implemented. A steady number of students remain interested in neurosurgery, with an increased number of women entering the field. Attention to wellness, in addition to high-quality education, should be further assessed as a factor to improve the overall NSR training and retention rate.

Platelet Aggregability as a Predictor of Restenosis Following Carotid Endarterectomy.

BACKGROUND: Antiplatelet drugs are administered before and after carotid endarterectomies (CEAs), but their efficacy for preventing restenosis remains unclear. Hence, this study aimed to identify associations between postoperative restenosis and platelet aggregability in CEA patients. METHODS: Thirty-six consecutive CEA patients treated at Tokyo Women's Medical University from May 2013 to March 2015 were included in this retrospective study. Restenosis was defined as a stenosis ratio greater than or equal to 50% per the European Carotid Surgery Trial criteria or peak systolic velocity of 150 cm/s on carotid ultrasound. Platelet aggregability was measured turbidimetrically using a light-transmission platelet aggregometer and analyzed in terms of aggregation profiles for 2 concentrations of collagen used to induce aggregation (.25 and 2.0 µg/mL). Patients were automatically divided into 9 classes (Class 1-9, from the lowest to the highest aggregability) using a software program according to area under their platelet aggregation curves. Each class was subdivided into 10 further gradations for a total of 90 possible scores (10-99) using a software program. Patients were divided into high- and low-platelet aggregability score groups (cut-off = 49). RESULTS: Data were analyzed for 36 of the 99 patients. Restenosis was observed in 10 (28%) patients. Restenosis incidence was significantly higher in patients with high-platelet aggregability score than in those with low-platelet aggregability score (50.0% [7/14] versus 13.6% [3 of 22]: P = .0176, odds ratio = 6.34, 95% CI: 1.27-31.57). CONCLUSIONS: Platelet aggregability is a useful metric for predicting and preventing restenosis after CEA. It has potential as an indicator for determining the optimal dose of antiplatelet drugs.

From sequence to function through structure: Deep learning for protein design.

The process of designing biomolecules, in particular proteins, is witnessing a rapid change in available tooling and approaches, moving from design through physicochemical force fields, to producing plausible, complex sequences fast via end-to-end differentiable statistical models. To achieve conditional and controllable protein design, researchers at the interface of artificial intelligence and biology leverage advances in natural language processing (NLP) and computer vision techniques, coupled with advances in computing hardware to learn patterns from growing biological databases, curated annotations thereof, or both. Once learned, these patterns can be used to provide novel insights into mechanistic biology and the design of biomolecules. However, navigating and understanding the practical applications for the many recent protein design tools is complex. To facilitate this, we 1) document recent advances in deep learning (DL) assisted protein design from the last three years, 2) present a practical pipeline that allows to go from de novo-generated sequences to their predicted properties and web-powered visualization within minutes, and 3) leverage it to suggest a generated protein sequence which might be used to engineer a biosynthetic gene cluster to produce a molecular glue-like compound. Lastly, we discuss challenges and highlight opportunities for the protein design field.

Neurostimulation success rate of repetitive-pulse focused ultrasound in an in vivo giant axon model: An acoustic parametric study.

PURPOSE: Focused ultrasound (FUS) is a promising tool to develop new modalities of therapeutic neurostimulation. The ability of FUS to stimulate the nervous system, in a noninvasive and spatiotemporally precise manner, has been demonstrated in animals and human subjects, but the underlying biomechanisms are not fully understood yet. The objective of the present study was to investigate the bioeffects involved in the generation of trains of action potentials (APs) by repetitive-pulse FUS stimuli in a simple invertebrate neural model. METHODS: The respective influences of different acoustic parameters on the neurostimulation success rate (NSR), defined as the rate of FUS stimuli capable of evoking at least one AP, were explored using the system of afferent nerves and giant fibers of Lumbricus terrestris as neural model. Each parameter was studied independently by administering random FUS sequences while keeping all but one FUS parameter constant. The NSR was evaluated as a function of (i) the spatial-average pulse-average intensity (Isapa ); (ii) the pulse duration (PD); (iii) the pulse repetition frequency (PRF); iv) the number of cycles per pulse (Ncycles ); (v) two ultrasound frequencies, f0  = 1.1 MHz and f3  = 3.3 MHz, corresponding to the fundamental and third-harmonic resonant frequencies of the FUS transducer, respectively (spherical, radius of curvature: 50 mm); and (vi) levels of emerging stable cavitation and inertial cavitation. RESULTS: The NSR associated to 1.1 MHz repetitive-pulse FUS stimuli was found to increase as a function of increasing Isapa , PD, PRF, and Ncycles . When evaluating each parameter at f = 1.1 MHz, it was observed that NSRs close to 100% were achieved when sufficiently elevating their respective values. When computing the NSR as a function of the spatial-average, temporal-average intensity (Isata ), defined as the product of PRF, PD, and Isapa , a significant elevation of the NSR from 0% to close to 100% was measured by increasing Isata from values approximate to 4 W/cm2 to values higher than 12 W/cm2 . No clear and consistent trend was observed in trials aimed at exploring the effects of different levels of stable and inertial acoustic cavitation on the NSR. Finally, the feasibility of inducing neural responses with 3.3 MHz repetitive-pulse FUS stimuli was also demonstrated with NSRs reaching up to 60%, in the range of FUS parameters studied. CONCLUSION: The time-averaged value of the radiation force per unit volume of tissue is proportional to the acoustic intensity. As a result, the observations from this study suggest that the neural structure responding to the stimulus is sensitive to the mean radiation force carried by the FUS sequence, regardless of the combination of FUS parameters giving rise to such force. The results from this study further revealed the existence of a minimal activation threshold with regard to Isapa .

Atrial fibrillation with rapid ventricular response as a maternal presentation of mirror syndrome: a case report.

Mirror syndrome is the phenomenon of fetal hydrops causing maternal edema and weight gain. Here, we report a case of arrhythmia as the primary maternal symptom. A 36-year-old woman, G2P1001, at 34.5 weeks of gestation presented with new-onset fetal hydrops combined with maternal weight gain and edema. She developed atrial fibrillation with rapid ventricular response; cardiac workup was unremarkable. Rate control was achieved with diltiazem. She underwent delivery and reverted to normal sinus rhythm on post-operative day 1. Volume overload causes atrial wall stress and neurohormonal changes that may trigger atrial fibrillation. Optimization with rate control facilitated good maternal and fetal outcomes in this case.

Stochastic neutral drifts seem prevalent in driving human virome assembly: Neutral, near-neutral and non-neutral theoretic analyses.

It is estimated that human body is inhabited by approximately 380 trillions of viruses, which exist in the form of viral communities and are collectively termed as human virome. How virome is assembled and what kind of forces maintain the composition and diversity of viral communities is still an open question. The question is of obvious importance because of its implications to human health and diseases. Here we address the question by harnessing the power of Hubbell's unified neutral theory of biodiversity (UNTB) in terms of three neutral models including standard Hubbell's neutral model (HNM), Sloan's near-neutral model (SNM) and Harris et al. (2017) multi-site neutral model (MSN), further augmented by Ning et al. (2019) normalized stochasticity ratio (NSR) and Hammal et al. (2015) power analysis for the neutral test (PNT). With the five models applied to 179 virome samples, we aim to obtain robust findings given both Type-I and Type-II errors are addressed and possible alternative, non-neutral processes are detected. It was found that stochastic neutral drifts seem prevalent: approximately 65-92% at metacommunity/landscape scales and 67-80% at virus species scale. The non-neutral selection is approximately 26-28% at community scale and 23% at species scale. The false negative rate is about 2-3%, which suggested rather limited confounding effects of non-neutral process on neutrality tests. We postulate that prevalence of neutrality in human virome is likely due to extremely simple structure of viruses (stands of DNA/RNA) and their inter-species homogeneities, forming the foundation of species equivalence-the hallmark of neutral theory.

A reciprocal translocation involving Aspergillus nidulans snxAHrb1/Gbp2 and gyfA uncovers a new regulator of the G2-M transition and reveals a role in transcriptional repression for the setBSet2 histone H3-lysine-36 methyltransferase.

Aspergillus nidulans snxA, an ortholog of Saccharomyces cerevisiae Hrb1/Gbp2 messenger RNA shuttle proteins, is-in contrast to budding yeast-involved in cell cycle regulation, in which snxA1 and snxA2 mutations as well as a snxA deletion specifically suppress the heat sensitivity of mutations in regulators of the CDK1 mitotic induction pathway. snxA mutations are strongly cold sensitive, and at permissive temperature snxA mRNA and protein expression are strongly repressed. Initial attempts to identify the causative snxA mutations revealed no defects in the SNXA protein. Here, we show that snxA1/A2 mutations resulted from an identical chromosome I-II reciprocal translocation with breakpoints in the snxA first intron and the fourth exon of a GYF-domain gene, gyfA. Surprisingly, a gyfA deletion and a reconstructed gyfA translocation allele suppressed the heat sensitivity of CDK1 pathway mutants in a snxA+ background, demonstrating that 2 unrelated genes, snxA and gyfA, act through the CDK1-CyclinB axis to restrain the G2-M transition, and for the first time identifying a role in G2-M regulation for a GYF-domain protein. To better understand snxA1/A2-reduced expression, we generated suppressors of snxA cold sensitivity in 2 genes: (1) loss of the abundant nucleolar protein Nsr1/nucleolin bypassed the requirement for snxA and (2) loss of the Set2 histone H3 lysine36 (H3K36) methyltransferase or a nonmethylatable histone H3K36L mutant rescued hypomorphic snxA mutants by restoring full transcriptional proficiency, indicating that methylation of H3K36 acts normally to repress snxA transcription. These observations are in line with known Set2 functions in preventing excessive and cryptic transcription of active genes.

Further Quantifying the Niche-Neutral Continuum of Human Digestive Tract Microbiomes with Near Neutral Model and Stochasticity Analysis.

It is postulated that the human digestive tract (DT) from mouth to intestine is differentiated into diverse niches. For example, Segata et al. discovered that the microbiomes of diverse habitats along the DT could be distinguished as 4 types (niches) including (i) stool; (ii) sub-gingival plaques (SubP) and supra-gingival plaques (SupP); (iii) tongue dorsum (TD), throat (TH), palatine tonsils (PT), and saliva (Sal); and (iv) hard palate (HP) and buccal mucosa (BM), and keratinized gingiva (KG). These niches are different not only in composition, but also in metabolic potentials. In a previous study, we applied Harris et al's multi-site neutral and Tang and Zhou's niche-neutral hybrid models to characterize the DT niches discovered by Segata et al. Here, we complement the previous study by applying Sloan's near-neural model and Ning et al's stochasticity analysis framework to quantify the niche-neutral continuum of the DT microbiome distribution to shed light on the possible ecological/evolutionary mechanism that shapes the continuum. Overall but excluding the stool site, the proportion of neutral OTUs (46%) is slightly higher than that of the positive selection (38%), but significantly higher than negative selection (15%). The gut (stool) exhibited 3 to 12 times lower neutrality than other DT sites. The analysis also cross-verified our previous hypothesis that the KG (keratinized gingiva) is of distinct assembly dynamics in the DT microbiome, should be treated as a fifth niche. Our findings offer new insight on the long-standing debate concerning whether a minimum of 2-mm of KG width is necessary for marginal periodontal health.

A study of Clinical Profile and in Hospital Outcomes of patients undergoing Percutaneous Transvenous Mitral Commissurotomy at a Tertiary Care Center of Nepal.

Introduction: Rheumatic heart disease (RHD), is a common cause of mitral stenosis (MS) in developing nations. As per current recommendation, Percutaneous Transvenous Mitral Commissurotomy (PTMC) is advised as a Class IA (I-Class Of Recommendation, COR; A-Level Of Evidence, LOE) indication in patients with symptomatic severe mitral stenosis. We aim to examine the clinical profile and in-hospital results of PTMC for mitral stenosis. Methods: A cross-sectional retrospective study was conducted at Manmohan Cardiothoracic Vascular and Transplant Center from April 2020 to May 2022. A structured questionnaire was used to collect the data and ethical approval for conducting the study was taken from the Institutional Review Committee (IRC) of Institute of Medicine (IOM). The data was collected in Microsoft Excel (Ver. 2013). For statistical analysis, SPSS 21 (IBM Corp. Released 2012. IBM SPSS Statistics for Windows, Version 21.0. Armonk, NY: IBM Corp.) Association was measured using a parametric and non-parametric test (depending upon the distribution of data) and p value < 0.05 was considered significant. Results: A total of 104 patients who met the inclusion criteria underwent PTMC during the study period. The mean age group of the patient was 41.7 ± 12.5 years, of which 23 (22.1%) were males and 81 (78.9%) were females. Mean mitral valve area prior to PTMC was 0.98 ± 0.19 mm2 that increased to 1.69 ± 0.19 mm2 after the procedure and it was statistically significant (p=<0.001). The post PTMC MVA varied with PTMC Wilkin's score with less than or equal to 8 having favorable outcomes. Conclusion: Successful PTMC is highly influenced by the patients' increasing age, valve morphology (calcification, thickness, mobility), Left atrial dimensions, Pre PTMC mitral valve area, Degree of Baseline mitral regurgitation. Post procedure development of MR is usually well tolerated but rarely be severe enough requiring surgical valve replacement.

Longitudinal Study of the Drug Resistance in Klebsiella pneumoniae of a Tertiary Hospital, China: Phenotypic Epidemiology Analysis (2013-2018).

PURPOSE: Multi-drug resistant Klebsiella pneumoniae (MDR KP) is spreading worldwide and has posed a huge medical burden to public health. However, studies on drug resistance surveillance of KP, especially MDR KP, with a large longitudinal sample size in a tertiary hospital are rare. This study aims to investigate phenotypic epidemiology characteristics of 4128 KP isolates in a Chinese tertiary hospital covering a period of 5 years. METHODS: All the KP clinical isolates were retrospectively collected from a tertiary hospital in Hunan province of China from Jan 5, 2013 to Jul 24, 2018. All the isolates were identified by MALDI-TOF MS analysis. Twenty-four antimicrobial agents were tested by antimicrobial susceptibility testing. Fisher exact test and logistic regression were used to analyze the association between clinical factors and antimicrobial non-susceptibility for seven second-choice antimicrobials. RESULTS: A total of 4128 KP isolates were collected in our study. The non-susceptible rates (NSRs) to ertapenem, imipenem and tigecycline increased considerably from 2013 to 2018 (13.6% to 28.6%, 10.1% to 28.9%, 10.8% to 46.5%, respectively). Amikacin presents the lowest NSR among 3 aminoglycosides (3.8-22.8%). The multi-drug NSRs among KP isolates to second-choice antimicrobials (88.6-100%) were higher than to all drugs (68.0%). The NSRs varied significantly among departments and sample sources. Higher ETP/IPM/AK NSRs (39.8/39.7/30.6%) were observed in Intensive Care Unit, and ETP/IPM non-susceptible isolates tended to distribute in cerebrospinal fluid. From 2015 to 2017, the NSRs of ETP, IPM, and AK showed an opposite trend of seasonal fluctuations to SXT. CONCLUSION: Higher multi-drug resistance (MDR) rates were observed in KP isolates to second-choice antimicrobials than to others, among which MDR rates to carbapenems or AK are the highest. A unique pattern of MIC and time distributions of MDR were observed. Clinical factors including gender were correlated with MDR rates of KP. Isolates in ICU and CSF showed higher NSRs in carbapenems which should be paid more attention to, and temporal distribution of NSRs was observed.

Simulation of Transit Transportation along the Northern Sea Route under Climate Change.

The article examines the problems and development prospects for the international transit of goods along the NSR. The existing restrictions on increasing freight traffic up to 80 million tons per year declared in program documents are identified. An option for its enhancement based on the domestic fleet of Arctic cargo ships is proposed. The article summarizes the main shortcomings of earlier studies assessing the transit capabilities of the NSR. A model for assessing the optimal number of ships for the transportation of goods is proposed taking into account climatic, physical-geographical, technological, and temporal constraints and risks. Within the framework of the model, the cost of goods transportation was estimated for implementing two scenarios of transit traffic.

Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis.

Lactococcus lactis cheese starter cultures typically contain a mix of many strains and may include variants that produce and/or tolerate the antimicrobial bacteriocin nisin. Nisin is well-established as an effective agent against several undesirable Gram-positive bacteria in cheese and various other foods. In the current study, we have examined the effect of nisin on 710 individual L. lactis strains during milk fermentations. Changes in milk acidification profiles with and without nisin exposure, ranging from unaltered acidification to loss of acidification, could be largely explained by the type(s) and variants of nisin immunity and nisin degradation genes present, but surprisingly, also by genotypic lineage (L. lactis ssp. cremoris vs. ssp. lactis). Importantly, we identify that nisin degradation by NSR is frequent among L. lactis and therefore likely the main mechanism by which dairy-associated L. lactis strains tolerate nisin. Insights from this study on the strain-specific effect of nisin tolerance and degradation during milk acidification is expected to aid in the design of nisin-compatible cheese starter cultures.

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes.

The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our 'new eyes,' are unraveling in real time the richness and magnitude of the plant RNA virosphere.