Short Insertions Research Articles

Treatment of Periprosthetic Joint Infection in Total Knee Arthroplasty with a Temporary Intramedullary Nail: Is a Long or Short Nail Better?

To our knowledge, no studies have compared postoperative outcomes between patients who received a temporary short or long intramedullary (IM) nail in the setting of infected total knee arthroplasty (TKA). Therefore, the aim of this study was to compare short-term outcomes for patients who underwent long or short IM nail insertion for treatment of periprosthetic knee infection. Specifically, we compared: (1) success rates; (2) patient reported/functional outcomes; and (3) complications between patients implanted with a short or a long IM nail following PJI of the knee. A retrospective chart review was performed for patients who underwent two-stage exchange arthroplasty with a temporary long or short IM nail between November 2010 and June 2018 at our institution (n = 67). Continuous and categorical variables were assessed using t-test/Mann-Whitney U test and chi-squared test, respectively. Logistic regression analyses were conducted to assess the effect of IM nail length on success rate while adjusting for age, sex, body mass index, and race. A total of 36 patients underwent temporary treatment with a long IM nail, while 31 patients received a short IM nail. There were no differences in success rate for reimplanted patients treated with long and short IM nails (odds ratio 0.992; p = 0.847). Fewer patients with a long IM nail went on to reimplantation (52.8 vs. 83.9%; p = 0.007). There was no difference in satisfaction (7.86 vs. 7.68; p = 0.515), pain scores (3.39 vs. 4.45 points; p = 0.126), or Knee Society score outcome scores (150.61 vs. 166.26 points; p = 0.117) between long or short IM nail patients. Following reimplantation, there was no difference in the number of patients who became reinfected (15.8 vs. 11.5%; p = 0.679) or went on to amputation (0 vs. 7.7%; p = 0.210). Periprosthetic joint infection (PJI) is a rare but serious postoperative complication following TKA. Our findings suggest that the use of long and short IM nails during two-stage exchange can have equal utility in PJI patients with severe bone defects.

Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas.

The Pacific oyster (Crassostrea gigas) is a widely distributed marine bivalve of great ecological and economic importance. In this study, we provide a high-quality chromosome-level genome assembled using Pacific Bioscience long reads and Hi-C-based and linkage-map-based scaffolding technologies and a high-resolution variation map constructed using large-scale resequencing analysis. The 586.8Mb genome consists of 10 pseudochromosome sequences ranging from 38.6 to 78.9Mb, containing 301 contigs with an N50 size of 3.1Mb. A total of 30,078 protein-coding genes were predicted, of which 22,757 (75.7%) were high-reliability annotations supported by a homologous match to a curated protein in the SWISS-PROT database or transcript expression. Although a medium level of repeat components (57.2%) was detected, the genomic content of the segmental duplications reached 26.2%, which is the highest among the reported genomes. By whole genome resequencing analysis of 495 Pacific oysters, a comprehensive variation map was built, comprised of 4.78 million single nucleotide polymorphisms, 0.60million short insertions and deletions, and 49,333 copy number variation regions. The structural variations can lead to an average interindividual genomic divergence of 0.21, indicating their crucial role in shaping the Pacific oyster genome diversity. The large amount of mosaic distributed repeat elements, small variations, and copy number variations indicate that the Pacific oyster is a diploid organism with an extremely high genomic complexity at the intra- and interindividual level. The genome and variation maps can improve our understanding of oyster genome diversity and enrich the resources for oyster molecular evolution, comparative genomics, and genetic research.

Population structure, case clusters, and genetic lesions associated with Canadian Salmonella 4,[5],12:i:- isolates.

Monophasic Salmonella 4,[5]:12:i:- are a major public health problem because they are one of the top five Salmonella serotypes isolated from clinical cases globally and because they can carry resistance to multiple antibiotics. A total of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium whole genome sequences (WGS) were generated. The various genetic lesions causing the Salmonella 4,[5]:12:i:- genotype were identified and assessed with regards to their distribution in the population of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium isolates, their geographical and temporal distribution, and their association with non-human sources. Several clades were identified in the population structure, and the largest two were associated almost exclusively with a short prophage insertion and insertion of a mobile element carrying loci encoding antibiotic and mercury resistance. IS26-mediated deletions and fljB point mutants appeared to spread clonally. 'Inconsistent' Salmonella 4,[5]:12:i:- isolates associated with specific, single amino acid changes in fljA and hin were found in a single clade composed of water, shellfish, and avian isolates. Inclusion of isolates from different case clusters identified previously by PFGE validated some of the clusters and invalidated others. Some wgMLST clusters of clinical isolates composed of very closely related isolates contained an isolate(s) with a different genetic lesion, suggesting continuing mobility of the implicated element responsible. Such cases may need to be left out of epidemiological investigations until sufficient numbers of isolates are included that statistical significance of association with sources is not impaired. Non-human sources were frequently found in or near clinical case clusters. Prospective surveillance and WGS of non-human sources and retrospective analysis by WGS of isolates from existing culture collections provides data critical for epidemiological investigations of food- and waterborne outbreaks.

Extending the L1 region in canonical double-stranded RNA-binding domains impairs their functions.

A large number of proteins involved in RNA metabolism possess a double-stranded RNA-binding domain (dsRBD), whose sequence variations and functional versatilities are still being recognized. All dsRBDs have a similar structural fold: α1-L1-β1-L2-β2-L3-β3-L4-α2 (α represents an α-helix, β a β-sheet, and L a loop conformation between the well-defined secondary structures). Our recent work revealed that the dsRBD in Drosha, which is involved in animal microRNA (miRNA) biogenesis, differs from other dsRBDs by containing a short insertion in its L1 region and that this insertion is important for Drosha function. We asked why the same insertion is excluded in all other dsRBDs and proposed that a longer L1 may be detrimental to their functions. In this study, to test this hypothesis, we inserted the Drosha sequence into several well-known dsRBDs from various organisms. Gel mobility shift assay demonstrated that L1 extension invariably reduced RNA binding by these dsRBDs. In addition, such a mutation in Dicer, another protein involved in miRNA biogenesis, impaired Dicer's ability to process miRNAs, which led to de-repression of reporter expression, in human cells. Taken together, our results add to the growing appreciation of the diversity in dsRBDs and suggest that dsRBDs have intricate structures and functions that are sensitive to perturbations in the L1 region.

McMillan electron lens in a system with space charge

Space charge (SC) forces of a circulating beam in a ring have both linear (defocusing) and nonlinear components, due to a nonuniform beam distribution. The linear component of SC forces produces a betatron tune shift, which is the largest for a zero-amplitude particle, while the nonlinear component produces an amplitude-dependent betatron tune spread. These SC effects are responsible for several undesirable phenomena in accelerators: emittance growth, particle losses, beam halo, etc. In this paper, we investigate the possibility to mitigate the distributed SC forces by a thin McMillan lens, providing an axially-symmetric kick, which is qualitatively opposite to the accumulated effect of beam's own SC. Experimentally, the proposed concept can be tested in Fermilab's IOTA ring. A thin McMillan lens can be implemented by a short (70) insertion of an electron beam with a specifically chosen density distribution in transverse directions. In this article, to test if McMillan lenses can reduce the tune spread induced by SC, we make several simulations with a 6-D particle tracking code, Synergia. We choose such beam and lattice parameters that the SC tune spread is roughly 0.5 and the emittance growth due to the half-integer resonance is clearly observed without the SC compensation. Then, we focus on reducing the emittance growth by adjusting the bare betatron tunes using the ring quadrupoles, and reducing the tune spread by the McMillan lenses. The results of reducing a large tune spread (≈ 0.5), reported here, are not perfect, but substantial. There is still room for further investigation. The simulations performed so far indicate that McMillan lenses can cope with an SC tune spread of ≈ 0.1 per lens.

ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules.

Structural variation (SV), which consists of genomic variation from 50 to millions of base pairs, confers considerable impacts on human diseases, complex traits and evolution. Accurately detecting SV is a fundamental step to characterize the features of individual genomes. Currently, several methods have been proposed to detect SVs using the next-generation sequencing (NGS) platform. However, due to the short length of sequencing reads and the complexity of SV content, the SV-detecting tools are still limited by low sensitivity, especially for insertion detection. In this study, we developed a novel tool, ClipSV, to improve SV discovery. ClipSV utilizes a read extension and spliced alignment approach to overcoming the limitation of read length. By reconstructing long sequences from SV-associated short reads, ClipSV discovers deletions and short insertions from the long sequence alignments. To comprehensively characterize insertions, ClipSV implements tree-based decision rules that can efficiently utilize SV-containing reads. Based on the evaluations of both simulated and real sequencing data, ClipSV exhibited an overall better performance compared to currently popular tools, especially for insertion detection. As NGS platform represents the mainstream sequencing capacity for routine genomic applications, we anticipate ClipSV will serve as an important tool for SV characterization in future genomic studies.

A comparative analysis of the mutagenicity of platinum-containing chemotherapeutic agents reveals direct and indirect mutagenic mechanisms

Platinum-based drugs are a mainstay of cancer chemotherapy. However, their mutagenic effect can increase tumour heterogeneity, contribute to the evolution of treatment resistance and also induce secondary malignancies. We coupled whole genome sequencing with phenotypic investigations on two cell line models to compare the magnitude and examine the mechanism of mutagenicity of cisplatin, carboplatin and oxaliplatin. Cisplatin induced significantly more base substitution mutations than carboplatin or oxaliplatin when used at equitoxic concentrations on human TK6 or chicken DT40 cells, and also induced the highest number of short insertions and deletions. The analysis of base substitution spectra revealed that all three tested platinum drugs elicit both a direct mutagenic effect at purine dinucleotides, and an indirect effect of accelerating endogenous mutagenic processes, whereas the direct mutagenic effect appeared to correlate with the level of DNA damage caused as assessed through histone H2AX phosphorylation and single-cell agarose gel electrophoresis, the indirect mutagenic effects were equal. The different mutagenicity and DNA-damaging effect of equitoxic platinum drug treatments suggest that DNA damage independent mechanisms significantly contribute to their cytotoxicity. Thus, the comparatively high mutagenicity of cisplatin should be taken into account in the design of chemotherapeutic regimens.

Ratpost: a searchable database of protein-inactivating sequence variations in 40 sequenced rat-inbred strains.

Rat-inbred strains are essential as scientific tools. We have analyzed the publicly available genome sequences of 40 rat-inbred strains and provide an overview of sequence variations leading to amino acid changes in protein-coding genes, premature STOP codons or loss of STOP codons, and short in-frame insertions and deletions of all protein-coding genes across all these inbred lines. We provide an overview of the predicted impact on protein function of all these affected proteins in the database, by comparing their sequence with the sequences of the rat reference strain BN/SsNHsdMcwi. We also investigate the flaws of the protein-coding sequences of this reference strain itself, by comparing them with a consensus genome. These data can be retrieved via a searchable website (Ratpost.be) and allow a global, better interpretation of genetic background effects and a source of naturally defective alleles in these 40 sequenced classical and high-priority rat-inbred strains.

MixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

BackgroundMulti-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data.ResultsThis study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested.ConclusionThe package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology.AvailabilityThe R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

Identification of four gastric cancer subtypes based on genetic analysis of cholesterogenic and glycolytic pathways

ABSTRACT Warburg phenomenon refers to the development of unique metabolic patterns during the growth of tumor cells. This study stratified gastric cancer into prognostic metabolic subgroups according to changes in gene expressions related to glycolysis and cholesterol synthesis. The RNA-seq expression data, single nucleotide variants (SNV), short insertions and deletions (InDel) mutation data, copy number variation (CNV) data and clinical follow-up information data of gastric cancer tissues were downloaded from The Cancer Genome Atlas (TCGA) database. ConsensusClusterPlus was used to stratify the metabolic subtypes of gastric cancer. Four metabolic subtypes (Cholesterogenic, Glycolytic, Mixed and Quiescent) of gastric cancer were identified, and patients with cholesterogenic tumors had the longest disease-specific survival (DSS). Genome-wide analysis showed that aberrant amplification of TP53 and MYC in gastric cancer was associated with abnormal cholesterol anabolic metabolism. The mRNA levels of mitochondrial pyruvate carriers 1 and 2 (MPC1/2) differed among the four subtypes. Tumors in the glycolytic group showed a higher PDCD1. A genomic signature based on tumor metabolism of different cancer types was established. This study showed that genes related to glucose and lipid metabolism play an important role in gastric cancer and facilitate a personalized treatment of gastric cancer.

Baska mask versus endotracheal tube in laparoscopic cholecystectomy surgery: a prospective randomized trial

ABSTRACT Background: Supraglottic airway devices have increasingly been used as the airway technique of choice in laparoscopic surgeries. This study compared the efficacy and safety of the Baska Mask with endotracheal tube (ETT) in patients undergoing elective laparoscopic cholecystectomy. Research design and methods: This single-center, prospective, randomized controlled trial recruited 60 patients aged 18–75 years with American Society of Anesthesiologists’ classifications I to III. The time taken to achieve effective airway, number of attempts, ease of insertion, ventilation parameters, hemodynamics data, and pharyngolaryngeal complications were recorded. Results: The time taken to achieve effective airway was shorter for the Baska group (26.6 ± 4.7 vs. 47.2 ± 11.8 s; p < 0.001), although the first-time insertion success rate was ≥90% for both groups. The ETT group experienced more pharyngolaryngeal complications, including cough, trauma, spasm, dysphonia, and sore throat, during device insertion and removal and had higher systolic and diastolic blood pressures during intubation (p = 0.001). The Baska Mask achieved significantly lower peak airway pressure (p = 0.024) with stable oropharyngeal leak pressure ≥33 cmH2O throughout the surgery. Conclusions: The Baska Mask is a suitable alternative to endotracheal intubation in selected patients undergoing laparoscopic cholecystectomy, with shorter insertion times, fewer perioperative complications, and improved ventilatory performance and hemodynamic response. Trial registration: The trial is registered at ClinicalTrials.gov (NCT03045835), 8 February 2017.

A Qualitative Study of Adult Hospitalized Patients With Difficult Venous Access Experiencing Short Peripheral Catheter Insertion in a Hospital Setting.

Hospitalized patients require venous access for procedures, treatments, or therapies. The short peripheral catheter (SPC) is one option for patients who need intravenous (IV) access for treatment. Patients with difficult vasculature sometimes require multiple attempts to obtain SPC access. The aim of this study was to gain an understanding of adult patients' experiences with SPC insertion, specifically those with difficult venous access. Ten participants were purposely sampled over a 2-month period for semistructured interviews from the medical, surgical, and telemetry units at an inner city, 750-bed trauma hospital in the southwestern United States. Four key themes developed from the interview data: skills and techniques of the clinicians, distress and the SPC insertion experience, physical and emotional pain, and patient/clinician communication. These themes provided ways that clinicians might improve the patient experience, including: ensuring experienced and confident inserters are available to insert SPCs, utilizing distraction and pain methods to decrease pain perception, communicating with patients regarding site selection and expectations during SPC insertion, and identifying patients with difficult vascular access to limit attempts per patient to preserve vascular sites.

A Minimally Invasive Technique for Short Spiral Implant Insertion with Contextual Crestal Sinus Lifting in the Atrophic Maxilla: A Preliminary Report.

The most recently reported techniques for the rehabilitation of the atrophic posterior maxilla are increasingly less invasive, as they are generally oriented to avoid sinus floor elevation with lateral access. The authors describe a mini-invasive surgical technique for short spiral implant insertion for the prosthetic rehabilitation of the atrophic posterior maxilla, which could be considered a combination of several previously described techniques based on the under-preparation of the implant site to improve fixture primary stability and crestal approach to the sinus floor elevation without heterologous bone graft. Eighty short spiral implants were inserted in the molar area of the maxilla in patients with 4.5–6 mm of alveolar bone, measured on pre-operative computed tomography. The surgical technique involved careful drilling for the preparation of implant sites at differentiated depths, allowing bone dislocation in the apical direction, traumatic crestal sinus membrane elevation, and insertion of an implant (with spiral morphology) longer than pre-operative measurements. Prostheses were all single crowns. In all cases, a spiral implant 2–4 mm longer than the residual bone was placed. Only two implants were lost due to peri-implantitis but subsequently replaced and followed-up. Bone loss values around the implants after three months (at the re-opening) ranged from 0 to 0.6 mm, (median value: 0.1 mm), while after two years, the same values ranged from 0.4 to 1.3 mm (median value: 0.7 mm). Clinical post-operative complications did not occur. After ten years, no implant has been lost. Overall, the described protocol seems to show good results in terms of predictability and patient compliance.

Radiological and Audiological Outcomes of the LISTENT LCI-20PI Cochlear Implant Device.

To study the surgical results, intracochlear position of the electrode array (EA) and auditory performance of the LISTENT LCI-20PI cochlear implant device, and daily use status at 3 years. A retrospective study. A single-tertiary referral center. Between January and December 2016, 20 patients underwent cochlear implantation using the LISTENT LCI-20PI (lateral wall EA). Cochlear implantation. Measurement of cochlear size, extent of posterior tympanotomy, and insertion depth. Scalar position of the EA evaluated by 3D reconstruction. Auditory outcomes 1 year after implantation and daily use status at 3 years. EAs were completely inserted in all cases with an insertion depth of 288 ± 36.8 degrees. One year later, the average sentence recognition score (SRS) was 90 ± 21.7%. EA scalar location was analyzed in 18 patients. Thirteen EAs (72.2%) were fully inserted into the scala tympani (ST) and 5 (27.8%) had shifted from the ST to the scala vestibuli (SV). There was no statistically significant difference in cochlear size, extent of posterior tympanotomy, or insertion depth between these two groups. EAs inserted by cochleostomy had a higher chance of scalar shift than those inserted via the round window (60% vs 15.4%, p = 0.099). SRS at 1 year with full ST insertion was significantly better than in those with scalar shift (99 ± 1.3% vs 83 ± 16.5%, p = 0.002). Three years after implantation, 92% of patients were daily users and 46% were telephone users. The LISTENT LCI-20PI provided accredited hearing rehabilitation with a short insertion depth. Full insertion into the ST was associated with better cochlear implantation outcomes.

Mutations and Copy Number Alterations in IDH Wild-Type Glioblastomas Are Shaped by Different Oncogenic Mechanisms.

Little is known about the mutational processes that shape the genetic landscape of gliomas. Numerous mutational processes leave marks on the genome in the form of mutations, copy number alterations, rearrangements or their combinations. To explore gliomagenesis, we hypothesized that gliomas with different underlying oncogenic mechanisms would have differences in the burden of various forms of these genomic alterations. This was an analysis on adult diffuse gliomas, but IDH-mutant gliomas as well as diffuse midline gliomas H3-K27M were excluded to search for the possible presence of new entities among the very heterogenous group of IDH-WT glioblastomas. The cohort was divided into two molecular subsets: (1) Molecularly-defined GBM (mGBM) as those that carried molecular features of glioblastomas (including TERT promoter mutations, 7/10 pattern, or EGFR-amplification), and (2) those who did not (others). Whole exome sequencing was performed for 37 primary tumors and matched blood samples as well as 8 recurrences. Single nucleotide variations (SNV), short insertion or deletions (indels) and copy number alterations (CNA) were quantified using 5 quantitative metrics (SNV burden, indel burden, copy number alteration frequency-wGII, chromosomal arm event ratio-CAER, copy number amplitude) as well as 4 parameters that explored underlying oncogenic mechanisms (chromothripsis, double minutes, microsatellite instability and mutational signatures). Findings were validated in the TCGA pan-glioma cohort. mGBM and “Others” differed significantly in their SNV (only in the TCGA cohort) and CNA metrics but not indel burden. SNV burden increased with increasing age at diagnosis and at recurrences and was driven by mismatch repair deficiency. On the contrary, indel and CNA metrics remained stable over increasing age at diagnosis and with recurrences. Copy number alteration frequency (wGII) correlated significantly with chromothripsis while CAER and CN amplitude correlated significantly with the presence of double minutes, suggesting separate underlying mechanisms for different forms of CNA.

Precise genome modification in tomato using an improved prime editing system.

The CRISPR/Cas-mediated genome editing technology has been widely applied to create knock-out alleles of genes by generating short insertions or deletions (indel) in various plant species. Due to the low efficiency of homology-directed repair (HDR) and difficulties in the delivery of DNA template for HDR, precise genome editing remains challenging in plants (Mao et al., 2019). A tandem repeat-HDR method was developed very recently for sequence replacement in rice, which is most useful for monocots (Lu et al., 2020). Base editors developed from Cas9 nickase fusion with cytosine and adenine deaminases enable targeted C-to-T or A-to-G substitutions, but are restricted to specific types of base replacements and target site selections (Mao et al., 2019).

ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy.

Somatic mutations in cancers affecting protein coding genes can give rise to potentially therapeutic neoepitopes. These neoepitopes can guide Adoptive Cell Therapies and Peptide- and RNA-based Neoepitope Vaccines to selectively target tumor cells using autologous patient cytotoxic T-cells. Currently, researchers have to independently align their data, call somatic mutations and haplotype the patient’s HLA to use existing neoepitope prediction tools. We present ProTECT, a fully automated, reproducible, scalable, and efficient end-to-end analysis pipeline to identify and rank therapeutically relevant tumor neoepitopes in terms of potential immunogenicity starting directly from raw patient sequencing data, or from pre-processed data. The ProTECT pipeline encompasses alignment, HLA haplotyping, mutation calling (single nucleotide variants, short insertions and deletions, and gene fusions), peptide:MHC binding prediction, and ranking of final candidates. We demonstrate the scalability, efficiency, and utility of ProTECT on 326 samples from the TCGA Prostate Adenocarcinoma cohort, identifying recurrent potential neoepitopes from TMPRSS2-ERG fusions, and from SNVs in SPOP. We also compare ProTECT with results from published tools. ProTECT can be run on a standalone computer, a local cluster, or on a compute cloud using a Mesos backend. ProTECT is highly scalable and can process TCGA data in under 30 min per sample (on average) when run in large batches. ProTECT is freely available at https://www.github.com/BD2KGenomics/protect.

Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways.

Genome analyses have documented that there are differences in gene repertoire between evolutionary distant lineages of the same bacterial species; however, less is known about microevolutionary dynamics of gene loss and acquisition within bacterial lineages as they evolve over years. Here, we analyzed the genomes of 45 Pseudomonas aeruginosa lineages evolving in the lungs of cystic fibrosis (CF) patients to identify genes that are lost or acquired during the first years of infection. On average, lineage genome content changed by 88 genes (range, 0 to 473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified convergent loss or acquisition of the same genes across lineages, suggesting selection for loss and acquisition of certain genes in the host environment. We found that a notable proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that the within-lineage variable genes (i.e., genes that had been lost or acquired during the infection) often belonged to genomic content not shared across all lineages. In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over years in a human host environment and provides a basis to further understand how gene loss and acquisition play roles in lineage differentiation and host adaptation.IMPORTANCE Bacterial airway infections, predominantly caused by P. aeruginosa, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we investigated P. aeruginosa within-host evolution with regard to gene loss and acquisition. We show that during long-term infection P. aeruginosa genomes tend to lose genes, in particular, genes related to virulence. This adaptive strategy allows reduction of the genome size and evasion of the host's immune response. This knowledge is crucial to understand the basic mutational steps that, on the timescale of years, diversify lineages and adds to the identification of bacterial genetic determinants that have implications for CF disease.

Evolutionary analysis of the Moringa oleifera genome reveals a recent burst of plastid to nucleus gene duplications

It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. The genome of Moringa oleifera, a fast-growing drought-tolerant orphan crop with highly valuable agronomical, nutritional and pharmaceutical properties, has recently been reported. We model here gene family evolution in Moringa as compared with ten other flowering plant species. Despite the reduced number of genes in the compact Moringa genome, 101 gene families, grouping 957 genes, were found as significantly expanded. Expanded families were highly enriched for chloroplastidic and photosynthetic functions. Indeed, almost half of the genes belonging to Moringa expanded families grouped with their Arabidopsis thaliana plastid encoded orthologs. Microsynteny analysis together with modeling the distribution of synonymous substitutions rates, supported most plastid duplicated genes originated recently through a burst of simultaneous insertions of large regions of plastid DNA into the nuclear genome. These, together with abundant short insertions of plastid DNA, contributed to the occurrence of massive amounts of plastid DNA in the Moringa nuclear genome, representing 4.71%, the largest reported so far. Our study provides key genetic resources for future breeding programs and highlights the potential of plastid DNA to impact the structure and function of nuclear genes and genomes.

A charge balancing technique for neurostimulators

A charge balancing technique that is applicable to dual-edge current nerve stimulators is proposed herein, which is primarily directed to achieving charge balance by controlling discharge times. Compared to the charge balancing technique proposed in other papers, the number of single-cycle imbalanced charges is less than 15 pC. In order to reduce the amount of imbalanced charge, indirect shunt technology, leakage current compensation technology and offset voltage compensation technology was proposed in this paper to build up a synchronization system. To ensure that the neural stimulator can still be in charge balance after performing multiple stimulation cycles, a short pulse insertion technique is applied to the circuit. The circuit was designed based on the TSMC 180 nm process and verified its functionality under the Cadence platform.