Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon

MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.     

Is Anterior Cervical Discectomy and Fusion Superior to Corpectomy and Fusion for Treatment of Multilevel Cervical Spondylotic Myelopathy? A Systemic Review and Meta-Analysis

Objective

Both anterior cervical discectomy with fusion (ACDF) and anterior cervical corpectomy with fusion (ACCF) are used to treat cervical spondylotic myelopathy (CSM), however, there is considerable controversy as to whether ACDF or ACCF is the optimal treatment for this condition. To compare the clinical outcomes, complications, and surgical trauma between ACDF and ACCF for the treatment of CSM, we conducted a meta-analysis.

Methods

We conducted a comprehensive search in MEDLINE, EMBASE, PubMed, Google Scholar and Cochrane databases, searching for relevant controlled trials up to July 2013 that compared ACDF and ACCF for the treatment of CSM. We performed title and abstract screening and full-text screening independently and in duplicate. A random effects model was used for heterogeneous data; otherwise, a fixed effect model was used to pool data, using mean difference (MD) for continuous outcomes and odds ratio (OR) for dichotomous outcomes.

Results

Of 2157 citations examined, 15 articles representing 1372 participants were eligible. Overall, there were significant differences between the two treatment groups for hospital stay (M = −5.60, 95% CI = −7.09 to −4.11), blood loss (MD = −151.35, 95% CI = −253.22 to −49.48), complications (OR = 0.50, 95% CI = 0.35 to 0.73) and increased lordosis of C2–C7 (MD = 3.70, 95% CI = 0.96 to 6.45) and fusion segments angles (MD = 3.38, 95% CI = 2.54 to 4.22). However, there were no significant differences in the operation time (MD = −9.34, 95% CI = −42.99 to 24.31), JOA (MD = 0.24, 95% CI = −0.10 to 0.57), VAS (MD = −0.06, 95% CI = −0.81 to 0.70), NDI (MD = −1.37, 95% CI  = −3.17 to 0.43), Odom criteria (OR = 0.88, 95% CI = 0.60 to 1.30) or fusion rate (OR = 1.17, 95% CI = 0.34 to 4.11).

Conclusions

Based on this meta-analysis, although complications and increased lordosis are significantly better in the ACDF group, there is no strong evidence to support the routine use of ACDF over ACCF in CSM.     

Leveraging vibration of effects analysis for robust discovery in observational biomedical data science

Hypothesis generation in observational, biomedical data science often starts with computing an association or identifying the statistical relationship between a dependent and an independent variable. However, the outcome of this process depends fundamentally on modeling strategy, with differing strategies generating what can be called “vibration of effects” (VoE). VoE is defined by variation in associations that often lead to contradictory results. Here, we present a computational tool capable of modeling VoE in biomedical data by fitting millions of different models and comparing their output. We execute a VoE analysis on a series of widely reported associations (e.g., carrot intake associated with eyesight) with an extended additional focus on lifestyle exposures (e.g., physical activity) and components of the Framingham Risk Score for cardiovascular health (e.g., blood pressure). We leveraged our tool for potential confounder identification, investigating what adjusting variables are responsible for conflicting models. We propose modeling VoE as a critical step in navigating discovery in observational data, discerning robust associations, and cataloging adjusting variables that impact model output.

COVID positivity and vitamin D intake, red meat and heart disease; how can we discern when biomedical associations are reliable and when they are susceptible to our own arbitrary choices and assumptions? This study presents “quantvoe,” a software package for exploring the entirety of possible findings due to the multiverse of associations possible.     

Squalamine analogues as potential anti-trypanosomal and anti-leishmanial compounds

This paper concerns the synthesis of various simplified analogues of the novel anti-microbial agent, squalamine. The compounds were then investigated for activity against Trypanosoma brucei, the causative agent of African trypanosomiasis, Trypanosoma cruzi, the causative agent of Chagas disease and Leishmania donovani, the causative agent of visceral leishmaniasis. Several compounds showed in vitro activity, especially against T. brucei and L. donovani. However, one compound showed poor in vivo activity.     

3D Topography of the Young Adult Anal Sphincter Complex Reconstructed from Undeformed Serial Anatomical Sections

Background

Pelvic-floor anatomy is usually studied by artifact-prone dissection or imaging, which requires prior anatomical knowledge. We used the serial-section approach to settle contentious issues and an interactive 3D-pdf to make the results widely accessible.

Method

3D reconstructions of undeformed thin serial anatomical sections of 4 females and 2 males (21–35y) of the Chinese Visible Human database.

Findings

Based on tendinous septa and muscle-fiber orientation as segmentation guides, the anal-sphincter complex (ASC) comprised the subcutaneous external anal sphincter (EAS) and the U-shaped puborectal muscle, a part of the levator ani muscle (LAM). The anococcygeal ligament fixed the EAS to the coccygeal bone. The puborectal-muscle loops, which define the levator hiatus, passed around the anorectal junction and inserted anteriorly on the perineal body and pubic bone. The LAM had a common anterior attachment to the pubic bone, but separated posteriorly into puborectal and “pubovisceral” muscles. This pubovisceral muscle was bilayered: its internal layer attached to the conjoint longitudinal muscle of the rectum and the rectococcygeal fascia, while its outer, patchy layer reinforced the inner layer. ASC contraction makes the ano-rectal bend more acute and lifts the pelvic floor. Extensions of the rectal longitudinal smooth muscle to the coccygeal bone (rectococcygeal muscle), perineal body (rectoperineal muscle), and endopelvic fascia (conjoint longitudinal and pubovisceral muscles) formed a “diaphragm” at the inferior boundary of the mesorectum that suspended the anorectal junction. Its contraction should straighten the anorectal bend.

Conclusion

The serial-section approach settled contentious topographic issues of the pelvic floor. We propose that the ASC is involved in continence and the rectal diaphragm in defecation.     

Belongingness in Early Secondary School: Key Factors that Primary and Secondary Schools Need to Consider

It is unknown if, and how, students redefine their sense of school belongingness after negotiating the transition to secondary school. The current study used longitudinal data from 266 students with, and without, disabilities who negotiated the transition from 52 primary schools to 152 secondary schools. The study presents the 13 most significant personal student and contextual factors associated with belongingness in the first year of secondary school. Student perception of school belongingness was found to be stable across the transition. No variability in school belongingness due to gender, disability or household-socio-economic status (SES) was noted. Primary school belongingness accounted for 22% of the variability in secondary school belongingness. Several personal student factors (competence, coping skills) and school factors (low-level classroom task-goal orientation), which influenced belongingness in primary school, continued to influence belongingness in secondary school. In secondary school, effort-goal orientation of the student and perception of their school’s tolerance to disability were each associated with perception of school belongingness. Family factors did not influence belongingness in secondary school. Findings of the current study highlight the need for primary schools to foster belongingness among their students at an early age, and transfer students’ belongingness profiles as part of the hand-over documentation. Most of the factors that influenced school belongingness before and after the transition to secondary are amenable to change.     

Advantages and Challenges of A Village Doctor-Based Cognitive Behavioral Therapy for Late-Life Depression in Rural China: A Qualitative Study

Background

The delivery of mental health services in rural China has been notably limited due to lack of qualified mental health professionals among other impeding factors. A village doctor-based cognitive behavioral therapy intervention may be one way of improving accessibility. The purpose of this study was to explore the advantages and challenges of implementing this intervention, as delivered by trained village doctors, to treat late-life depression in rural China.

Methods

We conducted one focus group discussion with 10 village doctors, 10 individual interviews with each of the village doctors, and individual interviews with 19 older adults. The topic guides were advantages and challenges of the intervention program from the perspective of the village doctors and older adults. Interviews were audio-recorded, transcribed, coded using NVivo 8, and analyzed using thematic analysis.

Results

The village doctors stressed the importance of role-playing and using instructive manuals in the training. Proper supervision was also a key component of the program. The benefits received from the intervention for the village doctors and the elders were positive such that both the doctors and the older adults were willing to implement/receive this intervention. Cultural and political factors (renqing and perceived policy consideration) facilitated the elders’ access to mental health services. Challenges included a lack of real therapy (in contrast to role-playing) demonstrated in the training and lack of a step-by-step manual based on different types of problems encountered. Other impediments to the successful implementation of the intervention included the time constraints of village doctors and the presence of other people when conducting the intervention.

Conclusions

The present study has demonstrated that the intervention program is likely to be an acceptable geriatric depression intervention in rural China if several challenges are appropriately addressed.     

Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients

Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.