Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation

Kenya’s black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management exercise translocated the survivors into four high security sanctuaries to control poaching and enhance breeding, and this measure successfully arrested the decline. Subsequently, new sanctuaries were established and the metapopulation size reached 650 animals by 2008. However, translocations and the current management strategy that partitions the metapopulation into ‘montane’ and ‘lowland’ rhinoceros may have substantial consequences at the population level and their impact on population genetic diversity has not been investigated. In this study, 12 of the 16 extant subpopulations were analysed using 408 bp of mitochondrial control region sequence (n = 170) and nine microsatellite loci (n = 145). Both markers detected moderate to high genetic diversity (h = 0.78 ± 0.027, n = 170; H_O = 0.70 ± 0.087, n = 145) consistent with previous studies on Diceros bicornis michaeli. However, mtDNA and nDNA diversity varied substantially between subpopulations. The results suggest that the Masai Mara is more differentiated, inbred and isolated than other subpopulations. It also suggests that there are neither distinct montane and lowland groups nor other detectable historical barriers to gene flow. Instead the large majority of genetic diversity was partitioned at the level of individuals; highlighting the need to conserve as many individuals as possible. Future translocations should consider the genetic profile of individuals and the demographic history of both the donor and recipient subpopulations.     

Impact of Daily Thermocycles on Hatching Rhythms,Larval Performance and Sex Differentiation of Zebrafish

In the wild, water temperature cycles daily: it warms up after sunrise, and cools rapidly after sunset. Surprisingly, the impact of such daily thermocycles during the early development of fish remains neglected. We investigated the influence of constant vs daily thermocycles in zebrafish, from embryo development to sexual differentiation, by applying four temperature regimens: two constant (24°C and 28°C) and two daily thermocycles: 28:24°C, TC (thermophase coinciding with daytime, and cryophase coinciding with night-time) and 24:28°C, CT (opposite to TC) in a 12:12 h light:dark cycle (LD). Embryo development was temperature-dependent but enhanced at 28°C and TC. Hatching rhythms were diurnal (around 4 h after lights on), but temperature- and cycle-sensitive, since hatching occurred sooner at 28°C (48 hours post fertilization; hpf) while it was delayed at 24°C (96 hpf). Under TC, hatching occurred at 72 hpf, while under CT hatching displayed two peaks (at 70 hpf and 94 hpf). In constant light (LL) or darkness (DD), hatching rhythms persisted with tau close to 24 h, suggesting a clock-controlled “gating” mechanism. Under 28°C or TC, larvae showed the best performance (high growth and survival, and low malformations). The sex ratio was strongly influenced by temperature, as the proportion of females was higher in CT and TC (79 and 83% respectively), contrasting with 28°C and 24°C, which led to more males (83 and 76%). Ovarian aromatase (cyp19a) expression in females was highest in TC and CT (6.5 and 4.6 fold higher than at 28°C, respectively); while anti-müllerian hormone (amh) expression in males increased in testis at 24°C (3.6 fold higher compared to TC) and particularly at 28°C (14.3 fold increase). Taken together, these findings highlight the key role of environmental cycles during early development, which shaped the daily rhythms in fish embryo and larvae, and ultimately influenced sex differentiation.     

You name it--memory and delay govern first name dynamics

The adoption and abandonment of first names through time is a fascinating phenomenon that may shed light on social dynamics and the forces that determine cultural taste in general. Here we show that baby name dynamics is governed almost solely by deterministic forces, even though the emerging abundance statistics resembles the one obtained from a pure drift model. Exogenous events are shown to affect the name dynamics very rarely, and most of the year-to-year fluctuations around the deterministic trend may be attributed solely to demographic noise. We suggest that the rise and fall of a name reflect an "infection" process with delay and memory. The symmetry between adoption and abandonment speed emerges from our model without further assumptions.     

Chloroplast DNA inheritance and variation in <Emphasis Type="Italic">Leucadendron</Emphasis> species (Proteaceae) as revealed by PCR-RFLP

The inheritance of chloroplast DNA (cpDNA) in Leucadendron species was studied by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis. A total of 100 progeny from five interspecific crosses involving seven parental species were tested, and all progeny exhibited the cpDNA restriction fragment pattern of the female parent, indicating that cpDNA in Leucadendron is maternally inherited. PCR-RFLP was also employed to study cpDNA variation among 21 Leucadendron species. Parsimony analysis using a heuristic search resulted in a phylogenetic tree that showed limited agreement to the taxonomic classification of Leucadendron species, based on morphological characteristics. The incongruence between cpDNA phylogenetic and taxonomic groupings in Leucadendron may be due to reticulate evolution involving a combination of hybridization and introgression, convergent evolution and/or lineage sorting at the interspecific, intersubsectional and intersectional levels.     

Adaptation to a high protein, carbohydrate-free diet induces a marked reduction of fatty acid synthesis and lipogenic enzymes in rat adipose tissue that is rapidly reverted by a balanced diet

We have previously shown that in vivo lipogenesis is markedly reduced in liver, carcass, and in 4 different depots of adipose tissue of rats adapted to a high protein, carbohydrate-free (HP) diet. In the present work, we investigate the activity of enzymes involved in lipogenesis in the epididymal adipose tissue (EPI) of rats adapted to an HP diet before and 12 h after a balanced diet was introduced. Rats fed an HP diet for 15 days showed a 60% reduction of EPI fatty acid synthesis in vivo that was accompanied by 45%-55% decreases in the activities of pyruvate dehydrogenase complex, ATP-citrate lyase, acetyl-CoA carboxylase, glucose-6-phosphate dehydrogenase, and malic enzyme. Reversion to a balanced diet for 12 h resulted in a normalization of in vivo EPI lipogenesis, and in a restoration of acetyl-CoA carboxylase activity to levels that did not differ significantly from control values. The activities of ATP-citrate lyase and pyruvate dehydrogenase complex increased to about 75%-86% of control values, but the activities of glucose-6-phosphate dehydrogenase and malic enzyme remained unchanged 12 h after diet reversion. The data indicate that in rats, the adjustment of adipose tissue lipogenic activity is an important component of the metabolic adaptation to different nutritional conditions.     

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools

Background  

Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here.     

A structural perspective on copper uptake in eukaryotes

Over a decade ago, genetic studies identified a family of small integral membrane proteins, commonly referred to as copper transporters (CTRs) that are both required and sufficient for cellular copper uptake in a yeast genetic complementation assay. We recently used electron crystallography to determine a projection density map of the human high affinity transporter hCTR1 embedded into a lipid bilayer. At 6 Å resolution, this first glimpse of the structure revealed that hCTR1 is trimeric and possesses the type of radial symmetry that traditionally has been associated with the structure of certain ion channels such as potassium or gap junction channels. Representative for this particular type of architecture, a region of low protein density at the center of the trimer is consistent with the existence of a copper permeable pore along the center three-fold axis of the trimer. In this contribution, we will briefly discuss how recent structure–function studies correlate with the projection density map, and provide a perspective with respect to the cellular uptake of other transition metals.     

In vitro production of bovine embryos in medium supplemented with a serum replacer: effects on blastocyst development, cryotolerance and survival to term

In this study, we evaluated a serum replacer (SR; Knockout SR, Invitrogen) in our in vitro culture systems. We hypothesized that SR would benefit bovine embryo development, since SR supported survival of embryonic stem cells (which originate from embryos). Experiment 1 compared oocyte maturation with SR versus fetal bovine serum (FBS). Following fertilization, blastocyst development was lower for oocytes matured with SR (21.5 versus 34.1, P<0.05). Experiment 2 evaluated SR for culturing embryos. Following fertilization, embryos were cultured for 3 days in KSOM, and then assigned to treatments: (1) KSOM static culture (KNM); (2) fresh KSOM (KD3); (3) KSOM+SR or (4) KSOM+FBS and cultured to Day 7 (fertilization=Day 0). Blastocyst development in FBS or SR was higher than either KNM or KD3 (48.2, 47.2, 32.7, and 35.5, respectively, P<0.05). Experiment 3 evaluated cryosurvival of embryos cultured in the same manner as Experiment 2. On Day 7, embryos were vitrified and upon warming, embryos cultured in SR had greater 24h survival rates (70.6%) than all other treatments (P<0.05). Finally, Experiment 4 evaluated effects of SR on pregnancy rate and development to term. Culture in SR was not detrimental to pregnancy or calving rates (50 and 50%, respectively), and SR calves had normal birth weights (mean=38.8 kg+/-1.5). In conclusion, the use of SR for maturation of oocytes was not beneficial; however, SR enhanced embryo culture by improving development in vitro, cryotolerance and survival, effectively replacing serum in culture.