The barley pan-genome reveals the hidden legacy of mutation breeding.

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.).

Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.

Powders to Thin Films: Advances in Conjugated Microporous Polymer Chemical Sensors.

Chemical sensing of harmful species released either from natural or anthropogenic activities is critical to ensuring human safety and health. Over the last decade, conjugated microporous polymers (CMPs) have been proven to be potential sensor materials with the possibility of realizing sensing devices for practical applications. CMPs found to be unique among other porous materials such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) due to their high chemical/thermal stability, high surface area, microporosity, efficient host-guest interactions with the analyte, efficient exciton migration along the π-conjugated chains, and tailorable structure to target specific analytes. Several CMP-based optical, electrochemical, colorimetric, and ratiometric sensors with excellent selectivity and sensing performance were reported. This review comprehensively discusses the advances in CMP chemical sensors (powders and thin films) in the detection of nitroaromatic explosives, chemical warfare agents, anions, metal ions, biomolecules, iodine, and volatile organic compounds (VOCs), with simultaneous delineation of design strategy principles guiding the selectivity and sensitivity of CMP. Preceding this, various photophysical mechanisms responsible for chemical sensing are discussed in detail for convenience. Finally, future challenges to be addressed in the field of CMP chemical sensors are discussed.

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes.

KEY MESSAGE: We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.

A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe.

Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) ⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.

Salivary leukocyte esterase activity by SillHa is a risk indicator of periodontal disease.

BACKGROUND: There is increasing evidence that diagnostic salivary tests measuring inflammatory biomarkers are being developed to assess inflammatory status for early detection, prevention, and progression of periodontal disease. Therefore, the aim of the present study was to investigate and identify the salivary biomarker that can predict the inflammatory status of periodontal disease. METHODS: A total of 36 patients (28 women and 8 men) with an average age of 57 years were investigated. Unstimulated saliva was collected from the recruited subjects and analyzed using SillHa, a saliva-testing device that measures bacteria count, saliva buffer capacity, acidity, leukocyte esterase, protein, and ammonia. Periodontal parameters were then obtained by clinical examination and initial periodontal therapy was performed. Data obtained with SillHa were compared with clinical periodontal parameters at baseline, re-examination (three months from baseline), and final examination (six months from re-examination). RESULTS: Leukocyte esterase activity in saliva measured by SillHa; BOP and PCR measured by clinical examination showed a significant difference between baseline and final examination and between re-examination and final examination. Patients in the lower median group (group 1) had a significant difference in leukocyte esterase activity between baseline and final examination and re-examination and final examination. In addition, patients in Group 1 had significantly lower BOP between baseline and final examination. While patients in the higher median group (group 2) showed a modest decrease in leukocyte esterase activity, which was significant only between baseline and final examination, no significant changes were observed concerning BOP. Furthermore, the associated systemic disease was observed in 30% and 81.2% of group 1 and 2 patients, respectively. CONCLUSION: The results suggest that leukocyte esterase activity in saliva measured by SillHa could serve as a reliable diagnostic marker for monitoring inflammatory status in periodontal disease.

A case series describing the risk of periodontal disease in Marfan syndrome patients harboring a possible aortic aneurysm or dissection.

BACKGROUND: Marfan syndrome (MFS) is a systemic disorder of connective tissues caused by insufficient elastic fiber formation that leads to structural weakness and results in various tissue disorders, including cardiovascular and periodontal disease. Notably however, the risk of periodontal disease in MFS patients affected by an aortic aneurysm or dissection has not yet been clarified. METHODS: We investigated the periodontal condition in the following three groups: MFS patients diagnosed with an aortic aneurysm or dissection with a planned aortic surgery (MFS surgery), MFS patients who had already undergone aortic surgery (MFS post-surgery) and healthy control patients (Healthy). The periodontal condition of all of these patients was evaluated at their first visit, reassessed again at two-month after the first visit, and evaluated again at a six-month follow-up after the reassessment. RESULTS: A total of 14 participants, 3 MFS surgery patients, 4 MFS post-surgery patients and 7 healthy control volunteers were examined. Saliva examinations revealed no significant differences between any of the groups at the first visit, reassessment, or follow-up. Interestingly, the MFS surgery cases showed a higher BOP and PISA at the first visit and follow-up compared with the other groups. In contrast, the MFS surgery patients showed an improvement in their LVDd and EF values, both markers of cardiac function, at the reassessment and follow-up compared with the first visit. CONCLUSIONS: MFS associated with an aortic aneurysm or dissection leads to a higher risk of periodontal disease, indicating the need for more frequent oral hygiene maintenance in these patients. In addition, MFS patients who undergo frequent professional cleaning of their teeth show a lower onset of cardiovascular disease, suggesting that professional oral hygiene in these cases contributes to a healthier condition.

Regulating Charge-Transfer in Conjugated Microporous Polymers for Photocatalytic Hydrogen Evolution.

Bandgap engineering in donor-acceptor conjugated microporous polymers (CMPs) is a potential way to increase the solar-energy harvesting towards photochemical water splitting. Here, the design and synthesis of a series of donor-acceptor CMPs [tetraphenylethylene (TPE) and 9-fluorenone (F) as the donor and the acceptor, respectively], F0.1 CMP, F0.5 CMP, and F2.0 CMP, are reported. These CMPs exhibited tunable bandgaps and photocatalytic hydrogen evolution from water. The donor-acceptor CMPs exhibited also intramolecular charge-transfer (ICT) absorption in the visible region (λmax =480 nm) and their bandgap was finely tuned from 2.8 to 2.1 eV by increasing the 9-fluorenone content. Interestingly, they also showed emissions in the 540-580 nm range assisted by the energy transfer from the other TPE segments (not involved in charge-transfer interactions), as evidenced from fluorescence lifetime decay analysis. By increasing the 9-fluorenone content the emission color of the polymer was also tuned from green to red. Photocatalytic activities of the donor-acceptor CMPs (F0.1 CMP, F0.5 CMP, and F2.0 CMP) are greatly enhanced compared to the 9-fluorenone free polymer (F0.0 CMP), which is essentially due to improved visible-light absorption and low bandgap of donor-acceptor CMPs. Among all the polymers F0.5 CMP with an optimum bandgap (2.3 eV) showed the highest H2 evolution under visible-light irradiation. Moreover, all polymers showed excellent dispersibility in organic solvents and easy coated on the solid substrates.

Highly fluorescent resorcinarene cavitand nanocapsules with efficient renal clearance.

Nanomaterial based imaging approaches hold substantial promise in addressing current diagnostic and therapeutic challenges. One of the key requirements for the successful clinical translation of nanomaterials is their complete clearance from the body within a reasonable time period preferably via the renal filtration route. This article describes the synthesis of highly fluorescent, water soluble, resorcinarene cavitand nanocapsules and demonstrates their effective renal clearance in mice. The synthesis and functionalization of nanocapsules was accomplished in a one-pot operation via thiol-ene reactions without involving self-assembly, sacrificial templates or emulsions. Water soluble resorcinarene cavitand nanocapsules obtained by this approach were covalently functionalized with Alexa Fluor 750. Highly fluorescent nanocapsules with hydrodynamic diameters of 122 nm and 68 nm and extinction coefficients of 1.3 × 10(9) M(-1) cm(-1) and 1.5 × 10(8) M(-1) cm(-1) respectively were prepared by varying the reaction conditions. The in vivo biodistribution and clearance of these nanocapsules in mice followed by whole-body fluorescence imaging showed that they were both cleared renally within a few hours. Given the inherent encapsulation capabilities of nanocapsules, the renal clearance demonstrated in this work opens up new opportunities for their theranostic applications especially for targeting and treating the urinary tract.

Direct oxidative pathway from amplex red to resorufin revealed by in situ confocal imaging.

Amplex Red (AR) is a very useful chemical probe that is employed in biochemical assays. In these assays, the non-fluorescent AR is converted to resorufin (RS), which strongly absorbs in the visible region (λabs = 572 nm) and yields strong fluorescence (λfluo = 583 nm). Even if AR is commonly used to report on enzymatic oxidase activities, an increasing number of possible interferences have been reported, thus lowering the accuracy of the so-called AR assay. As a redox-based reaction, we propose here to directly promote the conversion of AR to RS by means of electrochemistry. The process was first assessed by classic electrochemical and spectroelectrochemical investigations. In addition, we imaged the electrochemical conversion of AR to RS at the electrode surface by in situ confocal microscopy. The coupling of methodologies allowed to demonstrate that RS is directly formed from AR by an oxidation step, unlike what was previously reported. This gives a new insight in the deciphering of AR assays' mechanism and about their observed discrepancy.

C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses.

C2H2 type of zinc finger transcription factors (TFs) play crucial roles in plant stress response and hormone signal transduction. Hence considering its importance, genome-wide investigation and characterization of C2H2 zinc finger proteins were performed in Arabidopsis, rice and poplar but no such study was conducted in foxtail millet which is a C4 Panicoid model crop well known for its abiotic stress tolerance. The present study identified 124 C2H2-type zinc finger TFs in foxtail millet (SiC2H2) and physically mapped them onto the genome. The gene duplication analysis revealed that SiC2H2s primarily expanded in the genome through tandem duplication. The phylogenetic tree classified these TFs into five groups (I-V). Further, miRNAs targeting SiC2H2 transcripts in foxtail millet were identified. Heat map demonstrated differential and tissue-specific expression patterns of these SiC2H2 genes. Comparative physical mapping between foxtail millet SiC2H2 genes and its orthologs of sorghum, maize and rice revealed the evolutionary relationships of C2H2 type of zinc finger TFs. The duplication and divergence data provided novel insight into the evolutionary aspects of these TFs in foxtail millet and related grass species. Expression profiling of candidate SiC2H2 genes in response to salinity, dehydration and cold stress showed differential expression pattern of these genes at different time points of stresses.

FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets.

Foxtail millet has recently been regarded as a model crop for studying the systems biology of millets and bioenergy grass species. For expediting the functional genomic studies in this model crop as well as in the related millets and bioenergy grasses, we have developed a comprehensive transcription factor database. Our foxtail millet transcription factors database (FmTFDb: http://59.163.192.91/FmTFDb/index.html ) encompasses 2,297 putative TFs in 55 families along with its sequence features, chromosomal locations, tissue-specific gene expression data, gene ontology (GO) assignment, and phylogeny. FmTFDb is intended to provide the users an unrestricted public access in retrieving and visualizing the individual members of a TF family through a set of query interfaces and analysis tools, including the BLAST search, annotation query interfaces, and tools to identify enriched GO terms and to visualize physical maps. This FmTFDb will serve as a promising central resource for researchers as well as breeders who are dedicated towards crop improvement of millets and bioenergy grasses.

Optical microwell array for large scale studies of single mitochondria metabolic responses.

Microsystems based on microwell arrays have been widely used for studies on single living cells. In this work, we focused on the subcellular level in order to monitor biological responses directly on individual organelles. Consequently, we developed microwell arrays for the entrapment and fluorescence microscopy of single isolated organelles, mitochondria herein. Highly dense arrays of 3-µm mean diameter wells were obtained by wet chemical etching of optical fiber bundles. Favorable conditions for the stable entrapment of individual mitochondria within a majority of microwells were found. Owing to NADH auto-fluorescence, the metabolic status of each mitochondrion was analyzed at resting state (Stage 1), then following the addition of a respiratory substrate (Stage 2), ethanol herein, and of a respiratory inhibitor (Stage 3), antimycin A. Mean levels of mitochondrial NADH were increased by 29% and 35% under Stages 2 and 3, respectively. We showed that mitochondrial ability to generate higher levels of NADH (i.e., its metabolic performance) is not correlated either to the initial energetic state or to the respective size of each mitochondrion. This study demonstrates that microwell arrays allow metabolic studies on populations of isolated mitochondria with a single organelle resolution.

Monitoring metabolic responses of single mitochondria within poly(dimethylsiloxane) wells: study of their endogenous reduced nicotinamide adenine dinucleotide evolution.

It is now demonstrated that mitochondria individually function differently because of specific energetic needs in cell compartments but also because of the genetic heterogeneity within the mitochondrial pool-network of a cell. Consequently, understanding mitochondrial functioning at the single organelle level is of high interest for biomedical research, therefore being a target for analyticians. In this context, we developed easy-to-build platforms of milli- to microwells for fluorescence microscopy of single isolated mitochondria. Poly(dimethylsiloxane) (PDMS) was determined to be an excellent material for mitochondrial deposition and observation of their NADH content. Because of NADH autofluorescence, the metabolic status of each mitochondrion was analyzed following addition of a respiratory substrate (stage 2), ethanol herein, and a respiratory inhibitor (stage 3), Antimycin A. Mean levels of mitochondrial NADH were increased by 32% and 62% under stages 2 and 3, respectively. Statistical studies of NADH value distributions evidenced different types of responses, at least three, to ethanol and Antimycin A within the mitochondrial population. In addition, we showed that mitochondrial ability to generate high levels of NADH, that is its metabolic performance, is not correlated either to the initial energetic state or to the respective size of each mitochondrion.

Clinical trial of tooth desensitization prior to in-office bleaching.

The aim of this clinical trial was to compare tooth sensitivity during and after bleaching with hydrogen peroxide gel following application of GLUMA Desensitizer PowerGel or placebo. Forty-six subjects with sound maxillary incisors and canines were enrolled. Tooth shades were determined by comparison with a Vitapan Classic Shade guide. GLUMA Desensitizer PowerGel and placebo were randomly applied to the labial surfaces of the left or right anterior teeth for 1 min, which were then rinsed and dried. Then, Opalescence Boost PF 40% gel was applied onto labial enamel for 15 min. Sensitivity scores [recorded on a 10-point visual-analog scale (VAS)] were determined before, at 5, 10, and 15 min during, and 1, 24, 48 h and 1 wk after, the bleaching treatment. Shades were determined postbleaching and after 1 wk. Prebleaching application of GLUMA Desensitizer PowerGel significantly reduced tooth sensitivity during and after bleaching when compared with treatment with placebo. The whitening effects immediately and 1 wk after bleaching were significant when compared with the prebleaching shades. In conclusion, tooth pretreatment with GLUMA Desensitizer PowerGel for 1 min prior to 15 min of in-office bleaching with 40% hydrogen peroxide gel was highly effective in reducing tooth sensitivity during and after bleaching.

Assessment of forest fire emissions in Uttarakhand State, India, using Open Geospatial data and Google Earth Engine.

In the recent past, forest fires have increased due to the changing climate pattern. It is necessary to analyse and quantify various gaseous emissions so as to mitigate their harmful effects on air pollution. Satellite remote sensing data provides an opportunity to study the greenhouse gases in the atmosphere. The multispectral sensor of the Tropospheric Monitoring Instrument (Sentinel-5) is capable of recording the reflectance of wavelengths vital for measuring the atmospheric concentrations of methane, formaldehyde, aerosol, carbon monoxide, etc., at a spatial resolution of 0.01°. The present study utilized the Google Earth Engine (GEE) platform to study the emissions caused by forest fires in four districts of Uttarakhand State of India, which witnessed unprecedented fires in April-May 2021. All the datasets were ingested in GEE, which has the capability to analyse large datasets without the need to download them. The pre-fire period chosen was September 2020; the fire period was February-May 2021, and the post-fire period was June 2021. The variables chosen were aerosol absorbing index (AAI), carbon monoxide (CO) and nitrogen dioxide (NO2). The climate parameter temperature (Moderate Resolution Imaging Spectroradiometer Land Surface Temperature) and precipitation (from Climate Hazards Group InfraRed Precipitation (CHIRPS) Pentad) were also studied for the period mentioned. The results indicate a different trend for emissions in each district. For AAI, maximum emissions were noted in district Nainital followed by Almora, Tehri Garhwal and Garhwal. For CO emissions, the most affected district was Almora followed by Nainital, Garhwal and Tehri Garhwal. For NO2 emissions, the most affected district was Garhwal, followed by Nainital, Tehri Garhwal and Almora. Delta Normalized Burn Ratio was computed from Sentinel data (difference of pre-fire and post-fire images) to assess the burnt area severity. The Delta Normalized Burn Ratio values observed that the district with the most burnt area is Garhwal, followed by Nainital, Almora and Tehri Garhwal. The elevated temperatures and scanty rainfall patterns regulated the intensity and duration of forest fire. Monitoring the gaseous emissions as a consequence of forest fire in the GEE platform is much easier and more convenient at a regional level. Such data is much needed for mitigation measures to be implemented in time.

Hollow ring-like flexible electrode architecture enabling subcellular multi-directional neural interfacing.

Implantable neural microelectrodes for recording and stimulating neural activity are critical for research in neuroscience and clinical neuroprosthetic applications. A current need exists for developing new technological solutions for obtaining highly selective and stealthy electrodes that provide reliable neural integration and maintain neuronal viability. This paper reports a novel Hollow Ring-like type electrode to sense and/or stimulate neural activity from three-dimensional neural networks. Due to its unique design, the ring electrode architecture enables easy and reliable access of the electrode to three-dimensional neural networks with reduced mechanical contact on the biological tissue, while providing improved electrical interface with cells. The Hollow Ring electrodes, particularly when coated with the conducting polymer poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS), show improved electrical properties with extremely low impedance (7 MΩ µm2) and high charge injection capabilities (15 mC/cm2), when compared to traditional planar disk-type electrodes. The ring design also serves as an optimal architecture for cell growth to create an optimal subcellular electrical-neural interface. In addition, we showed that neural signals recorded by the ring electrode were better resolved than recordings from a traditional disk-type electrode improving the signal-to-noise ratio (SNR) and the burst detection from 3D neuronal networks in vitro. Overall, our results suggest the great potential of the hollow ring design for developing next-generation microelectrodes for applications in neural interfaces used in physiological studies and neuromodulation applications.

Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes.

Potato (Solanum tuberosum L.) is the most important non-grain food crop. Tandem duplication significantly contributes to genome evolution. The objectives of this study were to (i) identify tandemly duplicated genes and compare their genomic distributions across potato genotypes, (ii) investigate the bias in functional specificities, (iii) explore the relationships among coding sequence, promoter and expression divergences associated with tandemly duplicated genes, (iv) examine the role of tandem duplication in generating and expanding lineage-specific gene families, (v) investigate the evolutionary forces affecting tandemly duplicated genes, and (vi) assess the similarities and differences with respect to above mentioned aspects between cultivated genotypes and their wild-relative. In this study, we used well-annotated and chromosome-scale de novo genome assemblies of multiple potato genotypes. Our results showed that tandemly duplicated genes are abundant and dispersed through the genome. We found that several functional specificities, such as disease resistance, stress-tolerance, and biosynthetic pathways of tandemly duplicated genes were differentially enriched across multiple potato genomes. Our results indicated the existence of a significant correlation among expression, promoter, and protein divergences in tandemly duplicated genes. We found about one fourth of tandemly duplicated gene clusters as lineage-specific among multiple potato genomes, and these tended to localize toward centromeres and revealed distinct selection signatures and expression patterns. Furthermore, our results showed that a majority of duplicated genes were retained through sub-functionalization followed by genetic redundancy, while only a small fraction of duplicated genes was retained though neo-functionalization. The lineage-specific expansion of gene families by tandem duplication coupled with functional bias might have significantly contributed to potato's genotypic diversity, and, thus, to adaption to environmental stimuli.

Multi-ion-doped nano-hydroxyapatite-coated titanium intramedullary pins for long bone fracture repair in dogs-Clinical evaluation.

Plasma spray nano-hydroxyapatite-coated titanium intramedullary implants doped either with 5% zinc, 2.5% strontium, and 2.5% fluorine ions or with 5% zinc, 5% strontium, and 2.5% silver ions were evaluated compared with plasma spray nano-hydroxyapatite-coated titanium intramedullary implant and uncoated titanium intramedullary implants for open reduction and internal immobilization in 24 clinical cases of long bone fracture repair in dogs. Fracture-healing limb outcome was evaluated clinically, that is, radiographically. Biochemical estimation of serum calcium, serum phosphorus, alkaline phosphatase (ALP), and bone markers (bone ALP [BALP] and C-telopeptide of type 1 collagen [CTX]) was carried out on 0th day, 3rd week, 6th, and 9th week postoperatively. Multi-ion-doped plasma spray nano-hydroxyapatite-coated titanium intramedullary implants were found to be superior to plasma spray nano-hydroxyapatite-coated titanium intramedullary implants and uncoated titanium intramedullary implants in terms of all the parameters studied. Using plasma spray nano-hydroxyapatite-coated titanium implants doped with multi ions, that is, 5% zinc, 5% strontium, and 2.5% silver gave the best results in fracture repair followed by the implants doped with 5% zinc, 2.5% strontium, and 2.5% fluorine ions. Earliest and excellent limb usage with no postoperative complications was the hallmark of the use of these multi-ion-doped implants with higher serum calcium, serum phosphorus, ALP, BALP, and CTX values up to 3rd postoperative week and no lameness on the 21st day.

Correction of large jawbone defect in the mouse using immature osteoblast-like cells and a 3D polylactic acid scaffold.

Bone tissue engineering has been developed using a combination of mesenchymal stem cells (MSCs) and calcium phosphate-based scaffolds. However, these complexes cannot regenerate large jawbone defects. To overcome this limitation of MSCs and ceramic scaffolds, a novel bone regeneration technology must be developed using cells possessing high bone forming ability and a scaffold that provides space for vertical bone augmentation. To approach this problem in our study, we developed alveolar bone-derived immature osteoblast-like cells (HAOBs), which have the bone regenerative capacity to correct a large bone defect when used as a grafting material in combination with polylactic acid fibers that organize the 3D structure and increase the strength of the scaffold material (3DPL). HAOB-3DPL constructs could not regenerate bone via xenogeneic transplantation in a micromini pig alveolar bone defect model. However, the autogenic transplantation of mouse calvaria-derived immature osteoblast-like cells (MCOBs) isolated using the identical protocol for HAOBs and mixed with 3DPL scaffolds successfully regenerated the bone in a large jawbone defect mouse model, compared to the 3DPL scaffold alone. Nanoindentation analysis indicated that the regenerated bone had a similar micromechanical strength to native bone. In addition, this MCOB-3DPL regenerated bone possesses osseointegration ability wherein a direct structural connection is established with the titanium implant surface. Hence, a complex formed between a 3DPL scaffold and immature osteoblast-like cells such as MCOBs represents a novel bone tissue engineering approach that enables the formation of vertical bone with the micromechanical properties required to treat large bone defects.