Comparative analysis of multiple protein-sequence alignment methods [published erratum appears in Mol Biol Evol 1994 Sep;11(5):811]

We have analyzed a total of 12 different global and local multiple protein-sequence alignment methods. The purpose of this study is to evaluate each method's ability to correctly identify the ordered series of motifs found among all members of a given protein family. Four phylogenetically distributed sets of sequences from the hemoglobin, kinase, aspartic acid protease, and ribonuclease H protein families were used to test the methods. The performance of all 12 methods was affected by (1) the number of sequences in the test sets, (2) the degree of similarity among the sequences, and (3) the number of indels required to produce a multiple alignment. Global methods generally performed better than local methods in the detection of motif patterns.      

Exposure of human intestinal epithelial cells and primary human hepatocytes to trypsin-like serine protease inhibitors with potential antiviral effect

Human intestinal epithelial cell line-6 (HIEC-6) cells and primary human hepatocytes (PHHs) were treated with 3-amidinophenylalanine-derived inhibitors of trypsin-like serine proteases for 24 hours. It was proven that treatment with MI-1900 and MI-1907 was tolerated up to 50 μM in HIEC-6. These inhibitors did not cause elevations in extracellular H₂O₂ levels and in the concentrations of interleukin (IL)-6 and IL-8 and did not alter occludin distribution in HIEC-6. It was also found that MI-1900 and MI-1907 up to 50 μM did not affect cell viability, IL-6 and IL-8 and occludin levels of PHH. Based on our findings, these inhibitors could be safely applicable at 50 μM in HIEC-6 and in PHH; however, redox status was disturbed in case of PHH. Moreover, it has recently been demonstrated that MI-1900 prevents the replication and spread of the new SARS-CoV-2 in infected Calu-3 cells, most-likely via an inhibition of the membrane-bound host protease TMPRSS2.     

Bucking the trend: the African Black Oystercatcher as a recent conservation success story

The African Black Oystercatcher Haematopus moquini is a charismatic, southern African near-endemic, wader species, that is often seen as a flagship species for coastal bird conservation, as it was recently down-listed regionally to Least Concern on the IUCN Red List of Threatened Species. To celebrate this rare conservation success story, BirdLife South Africa named it the 2018 Bird of the Year and ran a year-long programme in collaboration with the Nature’s Valley Trust highlighting aspects of the species’ biology, current threats, and conservation success. We used data collected by the Southern African Bird Atlas Project (SABAP1 and SABAP2) to examine changes in the species’ range and relative abundance, both in the records between the two projects, as well as trends within the SABAP2 sampling period (2008–2017). This case study enabled us to assess whether such metrics can accurately reflect abundance and distributional changes in a species. We found increases in the reported range and the reporting rates between the two Atlas projects, and that the SABAP2 reporting rate was stable. Regionally, across four coastal categories, the reporting rate was lowest in KwaZulu-Natal, though this region also showed an increase in the probability of reporting during the SABAP2 period. While corroborating the recent change in the species’ conservation status, we also provide good evidence that the long-term SABAP data can be used successfully to assess population trends and range changes over time.     

Quantitative assessment of osseous, ocular, and periocular changes after hypertelorism surgery

The purpose of this study was to develop a methodology to quantify osseous, ocular, and periocular fat changes caused by correction of orbital hypertelorism to test the hypothesis that there is a quantitatively predictable relationship between the movement of the osseous orbit and that of the ocular globe. A retrospective review was performed of 10 patients who were status post unilateral or bilateral transcranial medial orbital translocation, for whom there were archival digital data for preoperative and postoperative (mean interval = 30 months) three-dimensional computed tomographic (CT) scans. In addition to standard demographic and surgical data, the clinical preoperative and postoperative interpupillary and intermedial canthal distances were recorded. By using a computer graphics workstation, the CT digital data were registered to four surgically unaltered anatomic fiducial points to allow longitudinal quantitative comparisons. The following three-dimensional measurements were made for each patient preoperatively and postoperatively: interdacryon and interocular centroid distances, and on a standard series of three horizontal and two vertical planes, the position of the medial and lateral orbital walls, and the thickness of the medial and lateral periorbital fat (20 orbits). CT digital distances were compared with similar clinical distances when possible. The age at operation ranged from 4.0 to 12.5 years (mean, 6.6 years). The reduction in interdacryon distance exceeded the reduction in intercentroid distance (mean interdacryon change = -5.3 mm versus mean intercentroid change = -2.7 mm). Although there was a strong correlation between the amount of reduction of the lateral orbital wall and intercentroid distances, there was only a moderate correlation between the reduction in the intercentroid distance and that of the medial orbital wall. Similarly, there was a moderate correlation between the decrease in thickness of the lateral periorbital fat and the reduction of intercentroid distance but not of the medial orbital fat. In conclusion, medial translocation of the orbit does not produce equivalent movement of the ocular globe; neither the intermedial canthal nor the interdacryon distance is a useful predictor of ocular centroid position; and if the goal of hypertelorism operation is reduction of interocular distance, then CT measurement of globe intercentroid distance is essential for outcome assessment.     

Long-term outcome of cleft lip nasal reconstruction in childhood

This study documents the pattern of unilateral cleft lip nasal reconstruction in the practice of one surgeon at a tertiary cleft center, evaluating the long-term appearance outcome of single-operation unilateral cleft lip nasal reconstruction in childhood. A retrospective medical record review was performed for all patients with a diagnosis of unilateral cleft lip and age greater than 15 years. Operative notes were reviewed, recording 15 variables identifying specific rhinoplastic maneuvers. Nasal appearance outcome analysis was performed for all patients who underwent only one nasal surgery before 12 years of age (n = 19). Standard frontal whole face photographic images were presented as opposing pairs in a looseleaf binder to two panels, 1 of 10 lay persons and 1 of 10 plastic surgeons. Each pair consisted of photographs of the same patient at different ages in one of three combinations: preoperative-perioperative, perioperative-longest postoperative, or preoperative-longest postoperative. Participants were asked to compare the appearance of the noses in the two photographs and assign a rating based on a 5-point Likert scale. Statistical analyses were performed on the data collected in the aesthetic analysis. The effect of surgery upon nasal appearance was assessed by comparing the preoperative and perioperative photographs. The effect of growth was assessed by comparing the perioperative and long-term postoperative photographs. The combined effect of surgery and growth was assessed by comparing the preoperative and long-term postoperative photographs. The data were assessed by lay and professional evaluators, together and separately, to determine whether differences existed. The majority of patients did not undergo revisional nasal surgery, whereas those who did usually had one nasal operation. Most revisional nasal surgery was performed in conjunction with other cleft-related secondary surgery. A majority of lay and professional evaluators perceived revisional nasal surgery as improving nasal appearance in the short-term and to a lesser degree in the long-term, as compared with the preoperative state. Evaluations of revisional nasal surgery are generally constant between the short-term and long-term postoperative images. Lay evaluations may be contaminated by a general decline in attractiveness with aging. Patient preference should be a major factor in the decision for nasal revision surgery. Multiple means of assessing nasal appearance outcome need to be used to validate results. Nasal appearance outcomes need to be correlated with outcomes with respect to nasal morphology and function as well as patient and parent satisfaction.     

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.      

Aerobic training increases the expression of adiponectin receptor genes in the peripheral blood mononuclear cells of young men

Little is known about the effect of exercise training on the expression of adiponectin receptor genes in peripheral blood mononuclear cells (PBMCs). In this study, we investigated the effects of aerobic training on the expression of AdipoR1 and AidpoR2 mRNAs in PBMCs, whole body insulin sensitivity, and circulating adiponectins in men. Thirty young men were randomly assigned to either a control (n=15) or an exercise (n=15) group. Subjects assigned to the exercise group underwent a 12-week jogging and/or running programme on a motor-driven treadmill at an intensity of 60%-75% of the age-based maximum heart rate with duration of 40 minutes per session and a frequency of 5 days per week. Two-way mixed ANOVA with repeated measures was used to test any significant time-by-group interaction effects for the measured variables at p=0.05. We found significant time-by-group interaction effects for waist circumference (p=0.001), VO_2max (p<0.001), fasting insulin (p=0.016), homeostasis model assessment for insulin resistance (HOMA-IR) (p=0.010), area under the curve (AUC) for insulin response during the 75-g oral glucose tolerance test (p=0.002), high-molecular weight (HMW) adiponectin (p=0.016), and the PBMC mRNA levels of AdipoR1 (p<0.001) and AdipoR2 (p=0.001). The exercise group had significantly increased mRNA levels of AdipoR1 and AdipoR2 in PBMCs, along with increased whole body insulin sensitivity and HMW adiponectin, decreased waist circumference, and increased VO_2max compared with the control group. In summary, the current findings suggest that exercise training modulates the expression of AdipoR1 and AdipoR2 mRNAs in PBMCs, implying that manipulation of the expression of these genes could be a potential surrogate for lifestyle intervention-mediated improvements of whole body insulin sensitivity and glucose homeostasis.     

Impact of limiting visual input on gait: Individuals with Parkinson disease,age-matched controls,and healthy young participants

Normal and limited vision gait was investigated in individuals with Parkinson disease (PD), healthy older and healthy young individuals. Participants walked a GAITRite mat with normal vision or vision of lower limbs occluded. Results indicate individuals with PD walked more slowly, with shorter and wider steps, and spent more time in double support with limited vision as compared to full vision. Healthy young and old individuals took shorter steps but were otherwise unchanged between conditions.