A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

Background

Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species.

Methodology and Principal Findings

(1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test.

Conclusions

We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus.     

The basement membrane microenvironment directs the normalization and survival of bioengineered human skin equivalents.

Epithelial-mesenchymal interactions promote the morphogenesis and homeostasis of human skin. However, the role of the basement membrane (BM) during this process is not well-understood. To directly study how BM proteins influence epidermal differentiation, survival and growth, we developed novel 3D human skin equivalents (HSEs). These tissues were generated by growing keratinocytes at an air-liquid interface on polycarbonate membranes coated with individual matrix proteins (Type I Collagen, Type IV Collagen or fibronectin) that were placed on contracted Type I Collagen gels populated with dermal fibroblasts. We found that only keratinocytes grown on membranes coated with the BM protein Type IV Collagen showed optimal tissue architecture that was similar to control tissues grown on de-epidermalized dermis (AlloDerm) that contained intact BM. In contrast, tissues grown on proteins not found in BM, such as fibronectin and Type I Collagen, demonstrated aberrant tissue architecture that was linked to a significant elevation in apoptosis and lower levels of proliferation of basal keratinocytes. While all tissues demonstrated a normalized, linear pattern of deposition of laminin 5, tissues grown on Type IV Collagen showed elevated expression of alpha6 integrin, Type IV Collagen and Type VII Collagen, suggesting induction of BM organization. Keratinocyte differentiation (Keratin 1 and filaggrin) was not dependent on the presence of BM proteins. Thus, Type IV Collagen acts as a critical microenvironmental factor in the BM that is needed to sustain keratinocyte growth and survival and to optimize epithelial architecture.     

Development of vesicular-arbuscular mycorrhizal infection and the uptake of immobile nutrients inLeucaena leucocephala

The level of vesicular-arbuscular mycorrhizal (VAM) infection in the roots of Leucaena grown in a sand-soil mixture in the greenhouse increased rapidly with time and reached a peak value of 84% at 30 days from planting. The pattern of immobile nutrient uptake and accumulation closely paralleled that of the development of infection, particularly during the first 10–30 days after planting. Significant changes in dry matter yield were also observed only after a significant portion of the root length was colonized byGlomus aggregatum. The development of VAM infection was not accompanied by growth depression at any of the sampling periods. However, VAM roots had very high levels of Cu which was not translocated to shoots. It is hypothesized that such a diversion of Cu by the endophyte from the host could cause growth depression under conditions where the soil volume is supplied with sub-optimal levels of Cu. Contribution from the Hawaii Institute of Tropical Agriculture and Human Resources Series No. 3186.     

Awareness and Attitude towards Breastfeeding among Two Generations of Indian Women: A Comparative Study

IntroductionPresent study was aimed to analyze the impact of education, employment and financial independence in breastfeeding practices among Indian women.MethodologyPresent explorative questionnaire based survey included 256 women (128 pairs) in the final analysis. A pair means – a) pregnant lady (in her third trimester) representing younger generation and b) her mother/mother in law representing the elder generation.ResultsWe found that the overall awareness regarding ‘breast milk’ being the best food for baby was excellent (overall 97.3%; younger generation: 96.9%; elder generation: 97.7%). Overall knowledge regarding the correct technique (28.9% younger generation and 21.9% elder generation) and frequency of breastfeeding (20.3% of younger generation and 34.4% of elder generation) was very poor. Less than 60% (younger generation: 57.8%; elder generation: 58.6%) were aware that the only major contraindication for breastfeeding is a mother infected with human immunodeficiency virus (HIV). On comparing responses obtained from the two generations of women, difference was not statistically significant among most of the issues related to breastfeeding. With regards to the attitude, despite better awareness, only 94.5% women in younger generation and 89.1% women in elder generation were planning to give mother’s milk as the first feed to the newborn. Similarly, less than 75% of women were ready to breast-feed the newborn immediately after birth. This was contradictory to the fact that 86% of pregnant women were aware that the baby should be breast-fed within an hour of birth.ConclusionAwareness with regards to breastfeeding issues had not changed significantly with the educational progress of Indian women. Despite the good level of awareness in the society regarding breastfeeding, attitude to practice the same is lacking.     

A neurological integrator for the oculomotor control system

This paper describes a mathematical model of a neurological integrator that has been developed to provide the very long leakage time constant required of the intgrator in the oculomotor system. The Gaussian distribution of cell thresholds and the eye-position- related discharge of the individual cells of the integrator model, and the highly specialized short-duration, high-frequency burst required of the input, have been modeled after the single-cell behavior actually observed in the oculomotor control areas of the brain stem of an alert primate.     

The evaluation of the radioprotective effect of Triphala (an ayurvedic rejuvenating drug) in the mice exposed to γ-radiation

The effect of 0, 5, 6.25, 10, 12.5, 20, 25, 40, 50 and 80 mg/kg b. wt. of aqueous extract of triphala (an Ayurvedic herbal medicine) administrered intraperitoneally was studied on the radiation-induced mortality in mice exposed to 10 Gy of gamma-radiation. Treatment of mice with different doses of triphala consecutively for five days before irradiation delayed the onset of mortality and reduced the symptoms of radiation sickness when compared with the non-drug treated irradiated controls. The highest protection against GI (gastrointestinal) death was observed for 12.5 mg/kg triphala, where a highest number of survivors were reported up to 10 days post-irradiation. While 10 mg/kg triphala i.p. provided the best protection as evidenced by the highest number of survivors after 30 days post-irradiation in this group when compared with the other doses of triphala. Toxicity study showed that triphala was non-toxic up to a dose of 240 mg/kg, where no drug-induced mortality was observed. The LD50 dose i.p. of triphala was found to be 280 mg/kg b. wt. Our study demonstrates the ability of triphala as a good radioprotective agent and the optimum protective dose of triphala was 1/28 of its LD50 dose.