Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop

<p>Abstract</p> <p>Background</p> <p>Concerted evolution has been believed to account for homogenization of genes within multigene families. However, the exact mechanisms involved in the homogenization have been under debate. Use of interspecific hybrid system allows detection of greater level of sequence variation, and therefore, provide advantage for tracing the sequence changes. In this work, we have used an interspecific hybrid system of scallop to study the sequence homogenization processes of rRNA genes.</p> <p>Results</p> <p>Through the use of a hybrid scallop system (<it>Chlamys farreri </it>♀ × <it>Argopecten irradians </it>♂), here we provide solid molecular and cellular evidence for homogenization of the rDNA sequences into maternal genotypes. The ITS regions of the rDNA of the two scallop species exhibit distinct sequences and thereby restriction fragment length polymorphism (RFLP) patterns, and such a difference was exploited to follow the parental ITS contributions in the F1 hybrid during early development using PCR-RFLP. The representation of the paternal ITS decreased gradually in the hybrid during the development of the hybrid, and almost diminished at the 14th day after fertilization while the representation of the maternal ITS gradually increased. Chromosomal-specific fluorescence <it>in situ </it>hybridization (FISH) analysis in the hybrid revealed the presence of maternal ITS sequences on the paternal ITS-bearing chromosomes, but not vice versa. Sequence analysis of the ITS region in the hybrid not only confirmed the maternally biased conversion, but also allowed the detection of six recombinant variants in the hybrid involving short recombination regions, suggesting that site-specific recombination may be involved in the maternally biased gene conversion.</p> <p>Conclusion</p> <p>Taken together, these molecular and cellular evidences support rapid concerted gene evolution via maternally biased gene conversion. As such a process would lead to the expression of only one parental genotype, and have the opportunities to generate recombinant intermediates; this work may also have implications in novel hybrid zone alleles and genetic imprinting, as well as in concerted gene evolution. In the course of evolution, many species may have evolved involving some levels of hybridization, intra- or interspecific, the sex-biased sequence homogenization could have led to a greater role of one sex than the other in some species.</p

Integrated Behavior Planning and Motion Control for Autonomous Vehicles with Traffic Rules Compliance

In this article, we propose an optimization-based integrated behavior planning and motion control scheme, which is an interpretable and adaptable urban autonomous driving solution that complies with complex traffic rules while ensuring driving safety. Inherently, to ensure compliance with traffic rules, an innovative design of potential functions (PFs) is presented to characterize various traffic rules related to traffic lights, traversable and non-traversable traffic line markings, etc. These PFs are further incorporated as part of the model predictive control (MPC) formulation. In this sense, high-level behavior planning is attained implicitly along with motion control as an integrated architecture, facilitating flexible maneuvers with safety guarantees. Due to the well-designed objective function of the MPC scheme, our integrated behavior planning and motion control scheme is competent for various urban driving scenarios and able to generate versatile behaviors, such as overtaking with adaptive cruise control, turning in the intersection, and merging in and out of the roundabout. As demonstrated from a series of simulations with challenging scenarios in CARLA, it is noteworthy that the proposed framework admits real-time performance and high generalizability.Comment: 7 pages, 5 figures, accepted for publication in The 2023 IEEE International Conference on Robotics and Biomimetics (ROBIO

Deep Learning for Person Reidentification Using Support Vector Machines

© 2017 Mengyu Xu et al. Due to the variations of viewpoint, pose, and illumination, a given individual may appear considerably different across different camera views. Tracking individuals across camera networks with no overlapping fields is still a challenging problem. Previous works mainly focus on feature representation and metric learning individually which tend to have a suboptimal solution. To address this issue, in this work, we propose a novel framework to do the feature representation learning and metric learning jointly. Different from previous works, we represent the pairs of pedestrian images as new resized input and use linear Support Vector Machine to replace softmax activation function for similarity learning. Particularly, dropout and data augmentation techniques are also employed in this model to prevent the network from overfitting. Extensive experiments on two publically available datasets VIPeR and CUHK01 demonstrate the effectiveness of our proposed approach

Texture Profile Analysis of Sliced Cheese in relation to Chemical Composition and Storage Temperature

The quantitative relationships among chemical composition, storage temperature, and texture of cheese were not fully understood. In this study, the effects of composition and temperature on textural properties of eight common varieties of sliced cheese were examined. The textural properties of sliced cheeses, including firmness, cohesiveness, adhesiveness, springiness, chewiness, and resilience, were measured by texture profile analysis after storage at 4 and 25 ∘ C for 4 h. Multivariate logistic regression models were established to describe the quantitative relationships of textural properties (dependent variables) to chemical composition and storage temperature (independent variables) of sliced cheeses. Results showed that protein, fat, moisture, and sodium chloride contents as well as storage temperature significantly affected the texture of sliced cheeses ( &lt; 0.05). In particular, fat in the dry matter and moisture in the nonfat substances were negatively correlated with firmness of sliced cheeses ( &lt; 0.05). As storage temperature rose from 4 to 25 ∘ C, the average values of firmness, chewiness, and resilience substantially declined by 42%, 45%, and 17%, respectively ( &lt; 0.05). This study provided reference data for adjusting chemical composition and storage temperature of common cheese products to obtain favorable texture for Chinese consumers, which thereby facilitated the localization of cheese industry in Chinese market

Fertilization and Cytogenetic Examination of Interspecific Reciprocal Hybridization between the Scallops, Chlamys farreri and Mimachlamys nobilis

Crossbreeding is a powerful tool for improving productivity and profitability in aquaculture. We conducted a pilot study of an artificial cross between two important cultivated scallops in China, Chlamys farreri and Mimachlamys nobilis, to test the feasibility of interspecific hybridization. Reciprocal hybridization experiments were performed using a single-pair mating strategy (M. nobilis ♀ × C. farreri ♂ and C. farreri ♀ × M. nobilis ♂). The fertilization of each pair was tracked using fluorescence staining of the gametes, and the chromosomes of the F1 hybrid larvae were examined via conventional karyotyping and genomic in situ hybridization (GISH). We observed moderate fertilization success in both interspecific crosses, although the overall fertilization was generally less rapid than that of intraspecific crosses. Conventional karyotyping showed that 70.4% of the viable F1 larvae in M. nobilis ♀ × C. farreri ♂ and 55.4% in C. farreri ♀ × M. nobilis ♂ comprised hybrid karyotypes (2n = 35 = 6m+5sm+11st+13t), and the results were further confirmed by GISH. Interestingly, we detected a few F1 from the M. nobilis ♀ × C. farreri ♂ cross that appeared to have developed gynogenetically. In addition, chromosome fragmentations, aneuploids and allopolyploids were observed in some F1 individuals. Our study presents evidence that the artificial cross between M. nobilis and C. farreri is experimentally possible. Further investigations of the potential heterosis of the viable F1 offspring at various developmental stages should be conducted to obtain a comprehensive evaluation of the feasibility of crossbreeding between these two scallop species

Enterovirus 71 induces degradation of TRIM38, a potential E3 ubiquitin ligase

<p>Abstract</p> <p>Background</p> <p>The tripartite motif (TRIM) proteins are a family of more than 70 members in human. However, only a few of them have been well studied. The TRIM proteins contain the conserved RING, B-box, coiled-coil, and SPRY domains, most of which are involved in protein ubiquitination. TRIM38 is a member of the TRIM protein family, which we studied in more detail here as its functions are largely unknown.</p> <p>Results</p> <p>Our study shows that, similar to other TRIM family members, TRIM38 is localized in the cytoplasm. TRIM38 increases ubiquitination of other cellular proteins and catalyzes self-ubiquitination. TRIM38 also promotes K63- and K48-linked ubiquitination of cellular proteins. An intact RING domain is important for the functions of TRIM38. In addition, enterovirus 71 infection induces TRIM38 degradation.</p> <p>Conclusions</p> <p>Our observations demonstrate that TRIM38 has E3 ubiquitin ligase activity and can be degraded during virus infection. These findings may provide insight into innate immune signaling pathways.</p

Molecular subgroups of adult medulloblastoma: a long-term single-institution study

Background Recent transcriptomic approaches have demonstrated that there are at least 4 distinct subgroups in medulloblastoma (MB); however, survival studies of molecular subgroups in adult MB have been inconclusive because of small sample sizes. The aim of this study is to investigate the molecular subgroups in adult MB and identify their clinical and prognostic implications in a large, single-institution cohort. Methods We determined gene expression profiles for 13 primary adult MBs. Bioinformatics tools were used to establish distinct molecular subgroups based on the most informative genes in the dataset. Immunohistochemistry with subgroup-specific antibodies was then used for validation within an independent cohort of 201 formalin-fixed MB tumors, in conjunction with a systematic analysis of clinical and histological characteristics. Results Three distinct molecular variants of adult MB were identified: the SHH, WNT, and group 4 subgroups. Validation of these subgroups in the 201-tumor cohort by immunohistochemistry identified significant differences in subgroup-specific demographics, histology, and metastatic status. The SHH subgroup accounted for the majority of the tumors (62%), followed by the group 4 subgroup (28%) and the WNT subgroup (10%). Group 4 tumors had significantly worse progression-free and overall survival compared with tumors of the other molecular subtypes. Conclusions We have identified 3 subgroups of adult MB, characterized by distinct expression profiles, clinical features, pathological features, and prognosis. Clinical variables incorporated with molecular subgroup are more significantly informative for predicting adult patient outcome

Extrusion of Dissolved Oxygen by Exopolysaccharide From Leuconostoc mesenteroides and Its Implications in Relief of the Oxygen Stress

Strains of Leuconostoc are generally facultatively anaerobic and exposure to oxygen might be detrimental; therefore, strategies to combat the oxygen stress are essential for these bacteria to survive and flourish in the oxygenic atmosphere. Despite the extensive applications in industry, the fundamental issues concerning the aerobic life of Leuconostocs remain to be addressed. In this study, we have demonstrated that Leuconostoc mesenteroides CGMCC10064 cultivated in sucrose medium would acquire a growth advantage over that in glucose medium under oxygenic conditions, as reflected by more viable cells and less accumulation of reactive oxygen species. Further analysis showed that the growth advantage was dependent on exopolysaccharide (EPS) synthesized by a secreted glucansucrase. Determination of the dissolved oxygen in the culture suggested that the growth improvement was mediated by extrusion of dissolved oxygen from the aqueous circumstances. Growth experiments performed with the purified EPS showed that supplementation of 5 g/L EPS in the medium could improve the aerobic growth of L. mesenteroides by ∼10-fold. Moreover, the purified EPS was also effective in promoting the aerobic growth of oxygen-sensitive Lactobacillus and Bifidobacterium. These results demonstrate that EPS of L. mesenteroides plays a critical role in relief of the oxygen stress, and suggest the potential of the EPS in manufacture as well as preservation of oxygen-sensitive probiotics

Chronic Kidney Disease Causes Disruption of Gastric and Small Intestinal Epithelial Tight Junction

BackgroundIntegrity of the tight junction (TJ) which seals the gap between the epithelial cells of the gastrointestinal tract is critical in preventing the entry of the microbial toxins, antigens, and other harmful products in the subepithelial tissues and the internal milieu. By enabling the absorption of these products, impairment of the intestinal epithelial barrier leads to local and systemic inflammation. We have recently found depletion of the key protein constituents of colonic epithelial TJ in animals with chronic kidney disease (CKD). Postmortem studies have revealed the presence of inflammation throughout the gastrointestinal tract in uremic humans. This observation suggests that uremia may cause disruption of the epithelial barrier in all segments of the gastrointestinal tract including the stomach, jejunum, and ileum. The present study was undertaken to explore this possibility.MethodsSprague-Dawley rats were randomized to CKD or control groups. The CKD group was subjected to 5/6 nephrectomy while the control group underwent a sham operation. The animals were observed for 10 weeks at which time they were euthanized and their stomachs, jejunums, and ileums were removed and processed for measurement of TJ proteins.ResultsThe CKD rats showed marked azotemia, systemic oxidative stress, and marked depletion of the key protein constituents of the epithelial TJ (claudin-1, occludin, and ZO1) in the stomach, jejunum, and ileum.ConclusionsThe present study extends the earlier finding of uremia-induced disruption of colonic epithelial TJ by documenting the involvement of the stomach, jejunum, and ileum as well