Synonymous Codon Usage Bias in Plant Mitochondrial Genes Is Associated with Intron Number and Mirrors Species Evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.     

Extraction Optimization,Characterization and Bioactivities of a Major Polysaccharide from Sargassum thunbergii

Sargassum thunbergii is a kind of natural edible algae. STP (S. thunbergii polysaccharides) was considered as the main bioactive compounds in S. thunbergii. To obtain the optimal processing conditions for maximum total sugar yield, single factor investigation and response surface methodology (RSM) were employed. The optimal processing conditions were as follows: liquid to solid ratio 120 mL/g, extraction time 210 min, extraction temperature 97°C. The experimental yield 7.53% under optimized conditions was closely agreed with the predicted yield 7.85% of the model. The major polysaccharide fraction from S. thunbergii (named STP-II) was purified by DEAE-Sepharose CL-6B column chromatography. High-performance size-exclusion chromatography (HPSEC), gas chromatography (GC) and high-performance liquid chromatography (HPLC) were used to identify its characterizations, and in vitro antioxidant assays and cytotoxicity assays were used to research its bioactivities. The purified fraction STP-II (63.75%) was a single peak in HPSEC with Sugar KS-804 column, had a molecular weight of 550KD, and comprised mainly of fucose, xylose, galactose, glucose and glucuronic acid. STP-II had higher scavenging activities on hydroxyl radical (76.72% at 0.7 mg/mL) and superoxide radical (95.17% at 2 mg/mL) than Vitamin C (Vc). STP-II also exhibited the capability of anti-proliferation in Caco-2 cells. STP-II possessed good antioxidant and inhibitory activity against human colon cancer Caco-2 cells in vitro and could be explored as novel natural functional food.     

MSI4/FVE is required for accumulation of 24-nt siRNAs and DNA methylation at a subset of target regions of RNA-directed DNA methylation

DNA methylation is an important epigenetic mark. In plants, de novo DNA methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. Researchers have previously inferred that a flowering regulator, MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE, is involved in non-CG methylation at several RdDM targets, suggesting a role of FVE in RdDM. However, whether and how FVE affects RdDM genome-wide is not known. Here, we report that FVE is required for DNA methylation at thousands of RdDM target regions. In addition, dysfunction of FVE significantly reduces 24-nucleotide siRNA accumulation that is dependent on factors downstream in the RdDM pathway. By using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that FVE directly binds to FVE-dependent 24-nucleotide siRNA cluster regions. Our results also indicate that FVE may function in RdDM by physically interacting with RDM15, a downstream factor in the RdDM pathway. Our study has therefore revealed that FVE, by associating with RDM15, directly regulates DNA methylation and siRNA accumulation at a subset of RdDM targets.     

Small Molecule Proprotein Convertase Inhibitors for Inhibition of Embryo Implantation

Uterine proprotein convertase (PC) 6 plays a critical role in embryo implantation and is pivotal for pregnancy establishment. Inhibition of PC6 may provide a novel approach for the development of non-hormonal and female-controlled contraceptives. We investigated a class of five synthetic non-peptidic small molecule compounds that were previously reported as potent inhibitors of furin, another PC member. We examined (i) the potency of these compounds in inhibiting PC6 activity in vitro; (ii) their binding modes in the PC6 active site in silico; (iii) their efficacy in inhibiting PC6-dependent cellular processes essential for embryo implantation using human cell-based models. All five compounds showed potent inhibition of PC6 activity in vitro, and in silico docking demonstrated that these inhibitors could adopt a similar binding mode in the PC6 active site. However, when these compounds were tested for their inhibition of decidualization of primary human endometrial stromal cells, a PC6-dependent cellular process critical for embryo implantation, only one (compound 1o) showed potent inhibition. The lack of activity in the cell-based assay may reflect the inability of the compounds to penetrate the cell membrane. Because compound''s lipophilicity is linked to cell penetration, a measurement of lipophilicity (logP) was calculated for each compound. Compound 1o is unique as it appears the most lipophilic among the five compounds. Compound 1o also inhibited another crucial PC6-dependent process, the attachment of human trophoblast spheroids to endometrial epithelial cells (a model for human embryo attachment). We thus identified compound 1o as a potent small molecule PC6 inhibitor with pharmaceutical potential to inhibit embryo implantation. Our findings also highlight that human cell-based functional models are vital to complement the biochemical and in silico analyses in the selection of promising drug candidates. Further investigations for compound 1o are warranted in animal models to test its utility as an implantation-inhibiting contraceptive drug.     

Equine antisperm antibodies (EASA): Preliminary study of the clinical response following breeding in immunized mares

Maiden mares (n=6), previously injected with stallion sperm cells (SC group, N=2), stallion seminal plasma (SP group, N=2), or phosphate-buffered saline as a control (C group, N=2) were followed through 5 consecutive estrous cycles to evaluate their clinical response when exposed to stallion sperm cells via breeding. Management was similar to that expected on typical breeding farms. The mares were teased daily and bred by artificial insemination (AI) in all 5 cycles. Differences in serum and uterine flushing equine antisperm antibody (EASA) levels, endometrial culture and cytology results, endometrial biopsy score and fertility were evaluated between treatment groups. An enzyme-linked immunosorbant assay (ELISA) was used to determine serum and uterine IgG and IgA levels specific for sperm cell or seminal plasma antigens. Serum IgG specific for sperm cell antigen was higher in the SC group than in the SP and C groups following exposure to sperm cells via breeding (P<0.05). All other EASA levels were not different between groups (P>0.05); however, uterine IgA levels in one of the SC treated mares did rise over all 5 cycles. No differences were detected in culture, cytology, biopsy or fertility results between groups (P>0.05). Changes in EASA levels were detected after breeding mares previously immunized with stallion sperm cells, however an associated clinical response was not apparent.     

A real-time computational model for estimating kinematics of ankle ligaments

Background: An accurate assessment of ankle ligament kinematics is crucial in understanding the injury mechanisms and can help to improve the treatment of an injured ankle, especially when used in conjunction with robot-assisted therapy. A number of computational models have been developed and validated for assessing the kinematics of ankle ligaments. However, few of them can do real-time assessment to allow for an input into robotic rehabilitation programs. Method: An ankle computational model was proposed and validated to quantify the kinematics of ankle ligaments as the foot moves in real-time. This model consists of three bone segments with three rotational degrees of freedom (DOFs) and 12 ankle ligaments. This model uses inputs for three position variables that can be measured from sensors in many ankle robotic devices that detect postures within the foot–ankle environment and outputs the kinematics of ankle ligaments. Validation of this model in terms of ligament length and strain was conducted by comparing it with published data on cadaver anatomy and magnetic resonance imaging. Results: The model based on ligament lengths and strains is in concurrence with those from the published studies but is sensitive to ligament attachment positions. Conclusions: This ankle computational model has the potential to be used in robot-assisted therapy for real-time assessment of ligament kinematics. The results provide information regarding the quantification of kinematics associated with ankle ligaments related to the disability level and can be used for optimizing the robotic training trajectory.