Optimization of a DNA-launched SARS-CoV-2 replicon with RNA splicing inhibitor Isoginkgetin.

We have previously developed a bacterial artificial chromosome (BAC)-vectored SARS-CoV-2 replicon, namely BAC-CoV2-Rep, which, upon transfection into host cells, serves as a transcription template for SARS-CoV-2 replicon mRNA to initiate replicon replication and produce nanoluciferase (Nluc) reporter from the subgenomic viral mRNA. However, an inherent issue of such DNA-launched replicon system is that the nascent full-length replicon transcript undergoes process by host RNA splicing machinery, which reduces replicon replication and generates spliced mRNA species expressing NLuc reporter independent of replicon replication. To mitigate this problem, we employed Isoginkgetin, a universal eukaryotic host splicing inhibitor, to treat cells transfected with BAC-CoV2-Rep. Isoginkgetin effectively increased the level of full-length replicon transcripts while concurrently reducing the level of Nluc signal derived from spliced replicon mRNA, making the Nluc reporter signal more correlated with replicon replication, as evidenced by treatment with known SARS-CoV-2 replication inhibitors including Remdesivir, GC376, and EIDD-1931. Thus, our study emphasizes that host RNA splicing is a confounding factor for DNA-launched SARS-CoV-2 replicon systems, which can be mitigated by Isoginkgetin treatment.

Benzalkonium chloride greatly deteriorates the biological activities of human corneal stroma fibroblasts in a concentration-dependent manner.

BACKGROUND: Corneal tissues indirectly obtain nutritional needs and oxygen to maintain their homeostasis, and therefore, benzalkonium chloride (BAC) containing ocular instillations for medical therapy may, in turn, induce toxic effects more than expected in corneal tissues, especially the inside stroma layer. METHODS: To evaluate the effects of very low concentrations (10-8%, 10-6%, or 10-4%) of BAC on human corneal stroma, we used two-dimensional (2D) cultures of human corneal stromal fibroblast (HCSF) cells and carried out the following analyses: (1) cell viability measurements, (2) Seahorse cellular bio-metabolism analysis, and (3) the expression of ECM molecules and endoplasmic reticulum (ER) stress-related molecules. RESULTS: In the absence and presence of 10-8%, 10-6%, or 10-4% concentrations of BAC, cell viability deteriorated and this deterioration was dose-dependent. The results showed that maximal mitochondrial respiration was decreased, the mRNA expression of most of ECM proteins was decreased, and ER stress-related molecules were substantially and dose-dependently down-regulated in HCSFs by the BAC treatment. CONCLUSIONS: The findings reported herein indicate that the presence of BAC, even at such low concentrations, is capable of causing the deterioration of cellular metabolic functions and negatively affecting the response to ER stress in HCSF cells resulting in a substantially decreased cellular viability.

Wearable Alcohol Monitoring Device for the Data-Driven Transcutaneous Alcohol Diffusion Model.

Wearable alcohol monitoring devices demand noninvasive, real-time measurement of blood alcohol content (BAC) reliably and continuously. A few commercial devices are available to determine BAC noninvasively by detecting transcutaneous diffused alcohol. However, they suffer from a lack of accuracy and reliability in the determination of BAC in real time due to the complex scenario of the human skin for transcutaneous alcohol diffusion and numerous factors (e.g., skin thickness, kinetics of alcohol, body weight, age, sex, metabolism rate, etc.). In this work, a transcutaneous alcohol diffusion model has been developed from real-time captured data from human wrists to better understand the kinetics of diffused alcohol from blood to different skin epidermis layers. Such a model will be a footprint to determine a base computational model in larger studies. Eight anonymous volunteers participated in this pilot study. A laboratory-built wearable blood alcohol content (BAC) monitoring device collected all the data to develop this diffusion model. The proton exchange membrane fuel cell (PEMFC) sensor was fabricated and integrated with an nRF51822 microcontroller, LMP91000 miniaturized potentiostat, 2.4 GHz transceiver supporting Bluetooth low energy (BLE), and all the necessary electronic components to build this wearable BAC monitoring device. The %BAC data in real time were collected using this device from these volunteers' wrists and stored in the end device (e.g., smartphone). From the captured data, we demonstrate how the volatile alcohol concentration on the skin varies over time by comparing the alcohol concentration in the initial stage (= 10 min) and later time (= 100 min). We also compare the experimental results with the outputs of three different input profiles: piecewise linear, exponential linear, and Hoerl, to optimize the developed diffusion model. Our results demonstrate that the exponential linear function best fits the experimental data compared to the piecewise linear and Hoerl functions. Moreover, we have studied the impact of skin epidermis thickness within ±20% and demonstrate that a 20% decrease in this thickness results in faster dynamics compared to thicker skin. The model clearly shows how the diffusion front changes within a skin epidermis layer with time. We further verified that 60 min was roughly the time to reach the maximum concentration, Cmax, in the stratum corneum from the transient analysis. Lastly, we found that a more significant time difference between BACmax and Cmax was due to greater alcohol consumption for a fixed absorption time.

An ensemble of regulatory elements controls Runx3 spatiotemporal expression in subsets of dorsal root ganglia proprioceptive neurons.

The Runx3 transcription factor is essential for development and diversification of the dorsal root ganglia (DRGs) TrkC sensory neurons. In Runx3-deficient mice, developing TrkC neurons fail to extend central and peripheral afferents, leading to cell death and disruption of the stretch reflex circuit, resulting in severe limb ataxia. Despite its central role, the mechanisms underlying the spatiotemporal expression specificities of Runx3 in TrkC neurons were largely unknown. Here we first defined the genomic transcription unit encompassing regulatory elements (REs) that mediate the tissue-specific expression of Runx3. Using transgenic mice expressing BAC reporters spanning the Runx3 locus, we discovered three REs-dubbed R1, R2, and R3-that cross-talk with promoter-2 (P2) to drive TrkC neuron-specific Runx3 transcription. Deletion of single or multiple elements either in the BAC transgenics or by CRISPR/Cas9-mediated endogenous ablation established the REs' ability to promote and/or repress Runx3 expression in developing sensory neurons. Our analysis reveals that an intricate combinatorial interplay among the three REs governs Runx3 expression in distinct subtypes of TrkC neurons while concomitantly extinguishing its expression in non-TrkC neurons. These findings provide insights into the mechanism regulating cell type-specific expression and subtype diversification of TrkC neurons in developing DRGs.

A Panel of Kaposi's Sarcoma-Associated Herpesvirus Mutants in the Polycistronic Kaposin Locus for Precise Analysis of Individual Protein Products.

Kaposi's sarcoma-associated herpesvirus (KSHV) is the cause of several human cancers, including the endothelial cell (EC) malignancy, Kaposi's sarcoma. Unique KSHV genes absent from other human herpesvirus genomes, the "K-genes," are important for KSHV replication and pathogenesis. Among these, the kaposin transcript is highly expressed in all phases of infection, but its complex polycistronic nature has hindered functional analysis to date. At least three proteins are produced from the kaposin transcript: Kaposin A (KapA), B (KapB), and C (KapC). To determine the relative contributions of kaposin proteins during KSHV infection, we created a collection of mutant viruses unable to produce kaposin proteins individually or in combination. In previous work, we showed KapB alone recapitulated the elevated proinflammatory cytokine transcripts associated with KS via the disassembly of RNA granules called processing bodies (PBs). Using the new ΔKapB virus, we showed that KapB was necessary for this effect during latent KSHV infection. Moreover, we observed that despite the ability of all kaposin-deficient latent iSLK cell lines to produce virions, all displayed low viral episome copy number, a defect that became more pronounced after primary infection of naive ECs. For ΔKapB, provision of KapB in trans failed to complement the defect, suggesting a requirement for the kaposin locus in cis. These findings demonstrate that our panel of kaposin-deficient viruses enables precise analysis of the respective contributions of individual kaposin proteins to KSHV replication. Moreover, our mutagenesis approach serves as a guide for the functional analysis of other complex multicistronic viral loci. IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) expresses high levels of the kaposin transcript during both latent and lytic phases of replication. Due to its repetitive, GC-rich nature and polycistronic coding capacity, until now no reagents existed to permit a methodical analysis of the role of individual kaposin proteins in KSHV replication. We report the creation of a panel of recombinant viruses and matched producer cell lines that delete kaposin proteins individually or in combination. We demonstrate the utility of this panel by confirming the requirement of one kaposin translation product to a key KSHV latency phenotype. This study describes a new panel of molecular tools for the KSHV field to enable precise analysis of the roles of individual kaposin proteins during KSHV infection.

Leukolectin-proteins are synthesized and secreted by lectocytes, a distinct category of fish embryonic mucus cells.

Fish perivitelline fluid (PVF) is a vital extra-embryonic compartment. At hatching, PVF-contents dissolve into the hatching fluid (HF). Analysis of Atlantic salmon HF reveals nearly a hundred distinct proteins, most of which were identified by advanced mass-spectrometry. However, one entity with an apparent molecular weight 26 kDa, necessitated identification from its tryptic peptides. Subsequent cloning and sequencing revealed novel leukolectin-proteins. From bioinformatic analysis, leukolectins (LL) belong in the tectonin protein-family, with recognized functions in innate immunity. This study aims to identify LL-expressing cells in diverse fish species, and to characterize the LL-gene in order to predict bio-functions of leukolectins. LL-proteins were detected in HF from several fish species and one invertebrate, using polyclonal LL-specific IgGs. Embryonic LL-immunoreactive cells were numerous in Atlantic salmon, rainbow trout, fewer in Atlantic cod, and rare in Atlantic halibut and Oikopleura dioica. LL-immunoreactive cells were termed lectocytes, which corresponded to peridermal mucuscells stained by PAS, but unstained by eosin. Hence, lectocytes and hatching-gland cells were clearly distinguished. Northern blots revealed two salmon LL-transcripts at mid-embryogenesis. Such transcripts were detected in epithelial cells of the periderm, gills and oral cavity. LL-transcripts predominated in the periderm, while choriolysin-transcripts were dominant in the gills. No co-expression of choriolysins and LL-transcripts was detected. BAC-library screening yielded salmon LL's genestructure with 4 introns, 5 exons, TATA-box, multiple upstream putative transcription-factor bindingsites and polyadenylation site. LL-gene location on chromosome ssa17 was identified in Ssal_v3.1, the 2021version of the salmon genome. In conclusion, larvae from several fish species are outfitted with mucus enriched by LL-proteins. Mucus cells are present in embryos of all fishes, but embryonic lectocyte-numbers are far higher in species with near total larval survival. When (maternal) chorionic first-line immuno-defence is lost at hatching, leukolectin-enriched mucus may provide vital protection for larvae.

Control of Pre-formed Halogenated Disinfection Byproducts with Reuse Biofiltration.

Disinfection byproduct (DBP) pre-formation is a major issue when prechlorination is used before or during advanced treatment of impacted drinking water sources. Control strategies for pre-formed DBPs before final disinfection, especially for currently nonregulated although highly toxic DBP species, are not yet established. This study evaluated the biodegradation potential of pre-formed DBPs, including haloacetonitriles (HANs), haloacetamides (HAMs), and haloacetaldehydes (HALs), during biofiltration with sand, anthracite, and biological activated carbon of three wastewater effluents under potable reuse conditions. Up to 90%+ removal of di- and trihalogenated HANs, HAMs, and HALs was observed, and removal was associated with active heterotrophic biomass and removal of biodegradable organic carbon. Unlike the microbial dehalogenation pathway of haloacetic acids (HAAs), removal of HANs and HAMs appeared to result from a biologically mediated hydrolysis pathway (i.e., HANs to HAMs and HAAs) that may be prone to inhibition. After prechlorination, biofiltration effectively controlled pre-formed DBP concentrations (e.g., from 271 µg/L to as low as 22 µg/L in total) and DBP-associated calculated toxicity (e.g., 96%+ reduction). Abiotic residual adsorption capacity in biological activated carbon media was important for controlling trihalomethanes. Overall, the toxicity-driving DBP species exhibited high biodegradation potential and biofiltration showed significant promise as a pre-formed DBP control technology.

Bubbleless Air Shapes Biofilms and Facilitates Natural Organic Matter Transformation in Biological Activated Carbon.

The biodegradation in the middle and downstream of slow-rate biological activated carbon (BAC) is limited by insufficient dissolved oxygen (DO) concentrations. In this study, a bubbleless aerated BAC (termed ABAC) process was developed by installing a hollow fiber membrane (HFM) module within a BAC filter to continuously provide aeration throughout the BAC system. The BAC filter without an HFM was termed NBAC. The laboratory-scale ABAC and NBAC systems operated continuously for 426 days using secondary sewage effluent as an influent. The DO concentrations for NBAC and ABAC were 0.78 ± 0.27 and 4.31 ± 0.44 mg/L, respectively, with the latter providing the ABAC with greater electron acceptors for biodegradation and a microbial community with better biodegradation and metabolism capacity. The biofilms in ABAC secreted 47.3% less EPS and exhibited greater electron transfer capacity than those in NBAC, resulting in enhanced contaminant degradation efficiency and long-term stability. The extra organic matter removed by ABAC included refractory substances with a low elemental ratio of oxygen to carbon (O/C) and a high elemental ratio of hydrogen to carbon (H/C). The proposed ABAC filter provides a valuable, practical example of how to modify the BAC technology to shape the microbial community, and its activity, by optimizing the ambient atmosphere.

Fine-Grained Intoxicated Gait Classification Using a Bilinear CNN.

Consuming excessive amounts of alcohol causes impaired mobility and judgment and driving accidents, resulting in more than 800 injuries and fatalities each day. Passive methods to detect intoxicated drivers beyond the safe driving limit can facilitate Just-In-Time alerts and reduce Driving Under the Influence (DUI) incidents. Popularly-owned smartphones are not only equipped with motion sensors (accelerometer and gyroscope) that can be employed for passively collecting gait (walk) data but also have the processing power to run computationally expensive machine learning models. In this paper, we advance the state-of-the-art by proposing a novel method that utilizes a Bi-linear Convolution Neural Network (BiCNN) for analyzing smartphone accelerometer and gyroscope data to determine whether a smartphone user is over the legal driving limit (0.08) from their gait. After segmenting the gait data into steps, we converted the smartphone motion sensor data to a Gramian Angular Field (GAF) image and then leveraged the BiCNN architecture for intoxication classification. Distinguishing GAF-encoded images of the gait of intoxicated vs. sober users is challenging as the differences between the classes (intoxicated vs. sober) are subtle, also known as a fine-grained image classification problem. The BiCNN neural network has previously produced state-of-the-art results on fine-grained image classification of natural images. To the best of our knowledge, our work is the first to innovatively utilize the BiCNN to classify GAF encoded images of smartphone gait data in order to detect intoxication. Prior work had explored using the BiCNN to classify natural images or explored other gait-related tasks but not intoxication Our complete intoxication classification pipeline consists of several important pre-processing steps carefully adapted to the BAC classification task, including step detection and segmentation, data normalization to account for inter-subject variability, data fusion, GAF image generation from time-series data, and a BiCNN classification model. In rigorous evaluation, our BiCNN model achieves an accuracy of 83.5%, outperforming the previous state-of-the-art and demonstrating the feasibility of our approach.

Role of feather reed grass (Calamagrostis acutiflora) in phytoremediation of urban soils.

Samples of soil and aerial mass of Calamagrostis acutiflora were obtained from an urban area adjacent to a street. The sampled material was analyzed to determine the content of Fe, Mn, Zn, Cu, Pb, Cd, Ni, Cr and Co, in addition to which soil was analyzed for the content of total organic carbon (TOC), salinity (EC) and reaction (pH). Based on the results, the enrichment factor (EF) and biological accumulation coefficient (BAC) of heavy metals as well as correlations between the analyzed characteristics were calculated. The content of heavy metals in the soil did not exceed the standards set for transportation areas, but the EF value implicated anthropogenic enrichment of soils with Zn, Cu, Pb, Cd and Co. Numerous, highly significant and positive correlations were obtained between the content of the elements in the soil, plants and in the soil-plant system, which suggests their relatively high bioavailability. The BAC values achieved for Co, Cr, Cu, Cd and Ni indicate that Calamagrostis acutiflora can be a useful species for phytoextraction of these elements from urban soils. Moreover, Calamagrostis acutiflora is a good choice for planting in urban areas due to its good adaptability, long growing season and tall conformation.

This study enabled us to the determine the usefulness of Calamagrostis acutiflora for phytoextraction of heavy metals (Fe, Mn, Zn, Cu, Pb, Cd, Ni, Cr and Co) from urban soils exposed to transportation pressure. This aspect of the said grass species has not been evaluated previously; meanwhile, owing to its high esthetic value, the grass can be an interesting choice in the landscaping of urban areas. The evaluation was based on determinations of the elements in the soil and in aerial biomass of Calamagrostis acutiflora sampled from an urban area adjacent to a busy street. The phytoremediation potential of Calamagrostis acutiflora was assessed according to the calculated biological accumulation coefficient (BAC). Furthermore, the enrichment factor (EF) for the heavy metals in the soil was determined, which enabled us to identify the extent of anthropogenic pressure in this area. Other determinations included basic soil physicochemical properties (TOC, pH, EC), which in practice will facilitate a choice of sites to be planted with Calamagrostis acutiflora in the future.

Lead-induced modification of growth and yield of Linum usitatissimum L. and its soil remediation potential.

This study was designed to evaluate the pre-reproductive and reproductive responses of Linum usitatissimum L. (flax, linseed plant) to different levels of Pb in the soil. Flax seeds were sown in garden soil-filled earthen pots and treated with three different levels of lead as lead chloride (150, 450, and 750 mg Pb kg-1 soil) except control, and each treatment was replicated three times. Growth and reproductive parameters and photosynthetic pigments were significantly reduced (p ≤ 0.05) for all treatments. Quantitatively, Chlorophyll b content decreased more than chlorophyll a and the amount of proline content in the leaves increased in lockstep with the increase of Pb levels in the soil. Pb was found in substantial amounts in the roots, shoots, and seeds. The pattern of Pb accumulation in different organs was root > shoot > seeds. Pb levels in seeds obtained from 750 mg Pb kg-1 soil-treated plants exceeded the permissible limits. Biological concentration factor (BCF), biological accumulation coefficient (BAC) and translocation factor (TF) values showed that roots of L. usitatissimum absorbed and accumulated a substantial quantity of Pb but translocated only a fraction of that to the shoots. Therefore, L. usitatissimum L. can be used in phytostabilization rather than phytoextraction of Pb.

This manuscript evaluates the potential of flaxseeds to cause biomagnification of lead (Pb) in the human body when grown under different concentrations of Pb and assessment of the risk posed to consumer health in a food chain. This study also provides insight to evaluate the uptake and extraction efficiency of Linum usitatissimum L. to remediate the Pb-polluted soil and use of Pb contaminated plant products (stem fibers and linseed oil) in an ecofriendly manner.

The association between breast arterial calcification and atherosclerotic cardiovascular disease in an Australian population-based breast cancer case-control study.

PURPOSE: Atherosclerotic cardiovascular disease (ASCVD) is a major cause of morbidity and mortality. Breast arterial calcification (BAC) on mammograms is not associated with breast cancer risk. However, there is increasing evidence supporting its association with cardiovascular disease (CVD). This study examines the association between BAC and ASCVD and their risk factors within an Australian population-based breast cancer study. MATERIALS AND METHODS: Data from the controls who participated in the breast cancer environment and employment study (BCEES) were linked with the Western Australian Department of Health Hospital Morbidity database and Mortality Registry to obtain ASCVD outcomes and related risk factor data. Mammograms from participants with no prior history of ASCVD were assessed for BAC by a radiologist. Cox proportional hazards regression was used to examine the association between BAC and later occurrence of an ASCVD event. Logistic regression was used to investigate the factors associated with BAC. RESULTS: A total of 1020 women with a mean age of 60 (sd = 7.0 years) were included and BAC found in 184 (18.0%). Eighty (7.8%) of the 1020 participants developed ASCVD, with an average time to event of 6.2 years (sd = 4.6) from baseline. In univariate analysis, participants with BAC were more likely to have an ASCVD event (HR = 1.96 95% CI 1.29-2.99). However, after adjusting for other risk factors, this association attenuated (HR = 1.37 95% CI 0.88-2.14). Increasing age (OR = 1.15, 95% CI 1.12-1.19) and parity (pLRT < 0.001) were associated with BAC. CONCLUSION: BAC is associated with increased ASCVD risk, but this is not independent of cardiovascular risk factors.

Mechanisms of Listeria monocytogenes Disinfection with Benzalkonium Chloride: From Molecular Dynamics to Kinetics of Time-Kill Curves.

Unravelling the mechanisms of action of disinfectants is essential to optimise dosing regimes and minimise the emergence of antimicrobial resistance. In this work, we examined the mechanisms of action of a commonly used disinfectant-benzalkonium chloride (BAC)-over a significant pathogen-L. monocytogenes-in the food industry. For that purpose, we used modelling at multiple scales, from the cell membrane to cell population inactivation. Molecular modelling revealed that the integration of the BAC into the membrane requires three phases: (1) the approaching of BAC to the cellular membrane, (2) the absorption of BAC to its surface, and (3) the integration of the compound into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilising the membrane. We hypothesised that the equilibrium of adsorption, although fast, was limiting for sufficiently large BAC concentrations, and a kinetic model was derived to describe time-kill curves of a large population of cells. The model was tested and validated with time series data of free BAC decay and time-kill curves of L. monocytogenes at different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to design novel disinfection processes rationally.

Blood alcohol concentration (BAC) for driving urgently should be lowered to 0.05.

On roadways in the USA, the highest risk of death and the highest economic costs result from alcohol-impaired driving. The National Academies of Sciences Engineering and Medicine has the stated goal, "Lowering the BAC limits set by state law is an evidence-based, poplulation-level intervention with widespread impact that could help reach a bold goal: zero deaths from drinking and driving." I provide scientific, empirical evidence from around the world that: (a) documents benefits from lowering the per se blood alcohol from 0.08% to 0.05%; and (b) I support this conclusion with a novel, graphical comparison showing logically that failing to support 0.05% BAC is based on giving priority to non-scientific criteria.

Sox10-cre BAC transgenes reveal temporal restriction of mesenchymal cranial neural crest and identify glandular Sox10 expression.

Diversity of neural crest derivatives has been studied with a variety of approaches during embryonic development. In mammals Cre-LoxP lineage tracing is a robust means to fate map neural crest relying on cre driven from regulatory elements of early neural crest genes. Sox10 is an essential transcription factor for normal neural crest development. A variety of efforts have been made to label neural crest derivatives using partial Sox10 regulatory elements to drive cre expression. To date published Sox10-cre lines have focused primarily on lineage tracing in specific tissues or during early fetal development. We describe two new Sox10-cre BAC transgenes, constitutive (cre) and inducible (cre/ERT2), that contain the complete repertoire of Sox10 regulatory elements. We present a thorough expression profile of each, identifying a few novel sites of Sox10 expression not captured by other neural crest cre drivers. Comparative mapping of expression patterns between the Sox10-cre and Sox10-cre/ERT2 transgenes identified a narrow temporal window in which Sox10 expression is present in mesenchymal derivatives prior to becoming restricted to neural elements during embryogenesis. In more caudal structures, such as the intestine and lower urinary tract, our Sox10-cre BAC transgene appears to be more efficient in labeling neural crest-derived cell types than Wnt1-cre. The analysis reveals consistent expression of Sox10 in non-neural crest derived glandular epithelium, including salivary, mammary, and urethral glands of adult mice. These Sox10-cre and Sox10-cre/ERT2 transgenic lines are verified tools that will enable refined temporal and cell-type specific lineage analysis of neural crest derivatives as well as glandular tissues that rely on Sox10 for proper development and function.

A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes.

Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.

BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris.

Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.

Contributions of the Human Cytomegalovirus UL30-Associated Open Reading Frames to Infection.

Transposon-based insertional mutagenesis screens have assessed how disruption of numerous human cytomegalovirus (HCMV) open reading frames (ORFs) impacts in vitro viral replication. Insertional mutagenesis of the HCMV UL30 gene was previously found to substantially inhibit production of viral progeny. However, there are a number of putative UL30-associated ORFs, and it is unclear how they impact viral replication. Here, we report on the contributions of the eight UL30-associated ORFs to infection. We find that deletion of the canonically annotated UL30 ORF substantially reduces production of infectious virus at both high and low multiplicities of infection (MOI). This deletion likely has complex effects on viral replication, as we find that it reduces the expression of neighboring non-UL30-associated ORFs. Mutation of the initiating methionine of the canonical UL30 ORF indicated that it is dispensable for high- and low-MOI infection in the highly passaged AD169 strain, although it is important for low-MOI infection in the less-passaged TB40/E strain. Comutation of eight methionines in the UL30 region results in a low-MOI viral replication defect, as does mutation of the TATA box responsible for the most abundant UL30 transcript, which is found to be necessary for the accumulation of multiple UL30-associated protein isoforms during infection. In total, our data indicate the importance of the UL30-associated ORFs during low-MOI HCMV infection and further highlight the difficulty associated with the functional interrogation of broadly disruptive mutations: e.g., large deletions or transposon insertions.IMPORTANCE Viral genes and their products are the critical determinants of viral infection. Human cytomegalovirus (HCMV) encodes many gene products whose roles during viral infection have not been assessed. Elucidation of the contributions that various HCMV gene products make to infection provides insight into the infectious program, which could potentially be used to limit HCMV-associated morbidity, a major issue during congenital infection and in immunosuppressed populations. Here, we explored the role of HCMV's UL30-associated gene products and found that they are important for HCMV replication. Future work elucidating the mechanisms through which they contribute to viral infection could highlight novel avenues for therapeutic intervention.

Reverse genetics systems for SARS-CoV-2.

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has caused severe public health crises and heavy economic losses. Limited knowledge about this deadly virus impairs our capacity to set up a toolkit against it. Thus, more studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) biology are urgently needed. Reverse genetics systems, including viral infectious clones and replicons, are powerful platforms for viral research projects, spanning many aspects such as the rescues of wild-type or mutant viral particles, the investigation of viral replication mechanism, the characterization of viral protein functions, and the studies on viral pathogenesis and antiviral drug development. The operations on viral infectious clones are strictly limited in the Biosafety Level 3 (BSL3) facilities, which are insufficient, especially during the pandemic. In contrast, the operation on the noninfectious replicon can be performed in Biosafety Level 2 (BSL2) facilities, which are widely available. After the outbreak of COVID-19, many reverse genetics systems for SARS-CoV-2, including infectious clones and replicons are developed and given plenty of options for researchers to pick up according to the requirement of their research works. In this review, we summarize the available reverse genetics systems for SARS-CoV-2, by highlighting the features of these systems, and provide a quick guide for researchers, especially those without ample experience in operating viral reverse genetics systems.

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae.

A Gram-stain-negative, non-motile and aerobic bacterium, designated HHU G3-2T, was isolated from surface water of the Yellow Sea, PR China. Strain HHU G3-2T was positive for oxidase activity and negative for catalase. Optimal growth occurred at 28 °C (range, 20-37 °C), pH 7.0 (range, pH 6.0-9.0) and in the presence of 2-5 % (w/v) NaCl (range, 1-7%). Phylogenetic analysis based on 16S rRNA gene sequences and 120 ubiquitous single-copy protein-coding genes indicated that strain HHU G3-2T formed a distinct phylogenetic lineage with Aestuariicella hydrocarbonica JCM 30134T, sharing a 16S rRNA gene sequence similarity of 98.05%. Average nucleotide identity and digital DNA-DNA hybridization values between strain HHU G3-2T and A. hydrocarbonica JCM 30134T were 75.74 and 17.80%, respectively, which were below the threshold values of 95-96 and 70 %, respectively. The DNA G+C content of the genomic DNA was 51.17 mol%. The major fatty acids (>10 %) were C17 : 1 ω8c (19.8 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 15.9 %), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 13.8 %) and C17 : 0 (10.3 %). The predominant isoprenoid quinone was ubiquinone-8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the polyphasic taxonomic data, strain HHU G3-2T represents a novel species of the genus Aestuariicella, for which the name Aestuariicella albida sp. nov. is proposed. The type strain is HHU G3-2T (=MCCC 1K04224T=JCM 34652T=GDMCC 1.2418T=CGMCC 1.17397T). In addition, we proposed the genus Aestuariicella as a member of the family Cellvibrionaceae.