Evolutionary history of two rare endemic conifer species from the eastern Qinghai–Tibet Plateau

Background and AimsUnderstanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai–Tibet Plateau (QTP).MethodsThe genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species.Key ResultsAnalyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter.ConclusionsThis study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.     

Inheritance of DNA Transferred from American Trypanosomes to Human Hosts

Interspecies DNA transfer is a major biological process leading to the accumulation of mutations inherited by sexual reproduction among eukaryotes. Lateral DNA transfer events and their inheritance has been challenging to document. In this study we modified a thermal asymmetric interlaced PCR by using additional targeted primers, along with Southern blots, fluorescence techniques, and bioinformatics, to identify lateral DNA transfer events from parasite to host. Instances of naturally occurring human infections by Trypanosoma cruzi are documented, where mitochondrial minicircles integrated mainly into retrotransposable LINE-1 of various chromosomes. The founders of five families show minicircle integrations that were transferred vertically to their progeny. Microhomology end-joining of 6 to 22 AC-rich nucleotide repeats in the minicircles and host DNA mediates foreign DNA integration. Heterogeneous minicircle sequences were distributed randomly among families, with diversity increasing due to subsequent rearrangement of inserted fragments. Mosaic recombination and hitchhiking on retrotransposition events to different loci were more prevalent in germ line as compared to somatic cells. Potential new genes, pseudogenes, and knockouts were identified. A pathway of minicircle integration and maintenance in the host genome is suggested. Thus, infection by T. cruzi has the unexpected consequence of increasing human genetic diversity, and Chagas disease may be a fortuitous share of negative selection. This demonstration of contemporary transfer of eukaryotic DNA to the human genome and its subsequent inheritance by descendants introduces a significant change in the scientific concept of evolutionary biology and medicine.     

Habitat structure and alarm call dialects in Gunnison's prairie dog (Cynomys gunnisoni)

We examined the relationship between habitat structure and alarmcall characteristics in six colonies of Gunnison's prairiedogs (Cynomys gunnisoni) near Flagstaff, Arizona, before andafter a mid-summer vegetation change. We found significantdifferences in alarm call characteristics between colonies,confirming the existence of alarm call dialects. Differencesin frequency components but not temporal components of callswere associated with differences in habitat structure. Playback experiments revealed that differences in alarm call structureaffected acoustic transmission of calls through the local habitat.Thus, we identify habitat structure as one factor that maycontribute to alarm call differences between colonies of Gunnison'sprairie dogs. Relationships between call characteristics andhabitat structure changed over seasons. Playback experimentssuggested that this changing relationship could reflect a change in the purpose of the alarm call between early and late summer.Some components of alarm calls seem tailored for attenuationover short distances in the early summer but for long-distancetransmission at summer's end. These differences might arisebecause pups stay close to their natal burrows in the earlysummer and disperse throughout a colony in late summer. Alternatively, these differences in alarm call transmission between seasonscould be caused by the increase in vegetation in the mid-summer.At the end of the summer prairie dogs could be more dependenton long-distance antipredator calls to offset the loss of visibilitycaused by the increase in vegetation in the late summer.     

High genetic diversity of in situ and ex situ populations of Madagascan coffee species: further implications for the management of coffee genetic resources

The genetic diversity of endemic Madagascan Coffea species has not received any considerable attention, despite the high extinction threat facing most of the species on the island. In order to address this shortfall, we assessed and compared the genetic diversity and allelic richness of ex situ and in situ populations for four selected species, and 18 ex situ populations maintained at the Kianjavato Coffee Research Station. We also investigated the possibility of in situ and ex situ hybridization events for Madagascan coffee, both within and between species. For these purposes, we used 18 nuclear microsatellite markers, on a total of 37 Coffea populations (4 in situ and 33 ex situ) representing a total of 398 genotypes (96 in situ and 302 ex situ) for 23 species. Our study showed (1) strong differentiation between Madagascan Coffea species; (2) good differentiation between all the populations studied, including those from the same locality (even when the area of the locality was restricted); (3) good evidence for both in situ and ex situ hybridization, although in situ hybridization appeared to be limited; (4) much higher genetic diversity within in situ collections compared to ex situ collections; and (5) that, despite limitations, the Kianjavato Coffee Research Station collection is an extremely valuable resource of Madagascan coffee germplasm. Recommendations for in situ and ex situ germplasm conservation are discussed.     

S-Allylcysteine, a garlic compound, protects against oxidative stress in 1-methyl-4-phenylpyridinium-induced parkinsonism in mice

S-Allylcysteine (SAC), the most abundant organosulfur compound in aged garlic extract, has multifunctional activity via different mechanisms and neuroprotective effects that are exerted probably via its antioxidant or free radical scavenger action. The 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated mouse has been the most widely used model for assessing neuroprotective agents for Parkinson's disease. 1-Methyl-4-phenylpyridinium (MPP⁺) is the stable metabolite of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, and it causes nigrostriatal dopaminergic neurotoxicity. Previous studies suggest that oxidative stress, via free radical production, is involved in MPP⁺-induced neurotoxicity. Here, we report on the neuroprotective effect of SAC against oxidative stress induced by MPP⁺ in the striatum of C57BL/6J mice. Mice were pretreated with SAC (125 mg/kg ip) daily for 17 days, followed by administration of MPP⁺ (0.72 mg/kg icv), and were sacrificed 24 h later to evaluate lipid peroxidation, different antioxidant enzyme activities, spontaneous locomotor activity and dopamine (DA) content. MPP⁺ administration resulted in a significant decrease in DA levels in the striatum. Mice receiving SAC (125 mg/kg ip) had significantly attenuated MPP⁺-induced loss of striatal DA levels (32%). The neuroprotective effect of SAC against MPP⁺ neurotoxicity was associated with blocked (100% of protection) of lipid peroxidation and reduction of superoxide radical production — indicated by an up-regulation of Cu-Zn-superoxide dismutase activity — both of which are indices of oxidative stress. Behavioral analyses showed that SAC improved MPP⁺-induced impairment of locomotion (35%). These findings suggest that in mice, SAC attenuates MPP⁺-induced neurotoxicity in the striatum and that an antioxidant effect against oxidative stress may be partly responsible for its observed neuroprotective effects.     

Lithium‐Pretreated Hard Carbon as High‐Performance Sodium‐Ion Battery Anodes

Hard carbon (HC) is the state‐of‐the‐art anode material for sodium‐ion batteries (SIBs). However, its performance has been plagued by the limited initial Coulombic efficiency (ICE) and mediocre rate performance. Here, experimental and theoretical studies are combined to demonstrate the application of lithium‐pretreated HC (LPHC) as high‐performance anode materials for SIBs by manipulating the solid electrolyte interphase in tetraglyme (TEGDME)‐based electrolyte. The LPHC in TEGDME can 1) deliver > 92% ICE and ≈220 mAh g^?1 specific capacity, twice of the capacity (≈100 mAh g^?1) in carbonate electrolyte; 2) achieve > 85% capacity retention over 1000 cycles at 1000 mA g^?1 current density (4 C rate, 1 C = 250 mA g^?1) with a specific capacity of ≈150 mAh g^?1, ≈15 times of the capacity (10 mAh g^?1) in carbonate. The full cell of Na₃V₂(PO₄)₃‐LPHC in TEGDME demonstrated close to theoretical specific capacity of ≈98 mAh g^?1 based on Na₃V₂(PO₄)₃ cathode, ≈2.5 times of the value (≈40 mAh g^?1) with nontreated HC. This work provides new perception on the anode development for SIBs.     

Intracellular signals involved in the effects of insulin-like growth factors and neuregulins on myofibre formation

A number of extracellular factors are involved in the embryonic development of skeletal muscle and the muscle regeneration that is triggered in response to muscle damage. Some of them, such as insulin-like growth factors (IGFs), fibroblast growth factors (FGFs), hepatocyte growth factor (HGF), transforming growth factor (TGF)-like molecules, leukemia inhibitor factor (LIF) or platelet-derived growth factors (PDGFs), are involved in the activation of cell proliferation that operates before muscle differentiation. In addition, factors such as IGFs, neuregulins (NRGs), sonic hedgehog (Shh) or Wnt promote muscle differentiation. Here, we review the intracellular signals that are triggered in the myogenic effect of IGFs and neuregulin and we describe common pathways. A fuller understanding of the signalling pathways triggered by these factors may permit the design of new tools for muscle regeneration therapy.     

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature‐related variables and divergent conditions for precipitation‐related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species. However, a precipitation regime different from those in Africa was directly involved in generating partial flowering overlap between species and thus in allowing hybridization and interspecific gene flow. Interspecific hybrids accounted for 4% of the mature individuals in the sympatric population and occurred between each pair of species with various level of introgression. Adaptation to new environmental conditions following introduction of Coffea species to New Caledonia has resulted in a secondary contact between three related species, which would not have happened in their native ranges, leading to hybridization and gene flow.     

Development of a Multiplex-PCR probe system for the proper identification of <Emphasis Type="Italic">Klebsiella variicola</Emphasis>

Background

Klebsiella variicola was very recently described as a new bacterial species and is very closely related to Klebsiella pneumoniae; in fact, K. variicola isolates were first identified as K. pneumoniae. Therefore, it might be the case that some isolates, which were initially classified as K. pneumoniae, are actually K. variicola. The aim of this study was to devise a multiplex-PCR probe that can differentiate isolates from these sister species.

Result

This work describes the development of a multiplex-PCR method to identify K. variicola. This development was based on sequencing a K. variicola clinical isolate (801) and comparing it to other K. variicola and K. pneumoniae genomes. The phylogenetic analysis showed that K. variicola isolates form a monophyletic group that is well differentiated from K. pneumoniae. Notably, the isolate K. pneumoniae 342 and K. pneumoniae KP5-1 might have been misclassified because in our analysis, both clustered with K. variicola isolates rather than with K. pneumoniae. The multiplex-PCR (M-PCR-1 to 3) probe system could identify K. variicola with high accuracy using the shared unique genes of K. variicola and K. pneumoniae genomes, respectively. M-PCR-1 was used to assay a collection of multidrug-resistant (503) and antimicrobial-sensitive (557) K. pneumoniae clinical isolates. We found K. variicola with a prevalence of 2.1% (23/1,060), of them a 56.5% (13/23) of the isolates were multidrug resistant, and 43.5% (10/23) of the isolates were antimicrobial sensitive. The phylogenetic analysis of rpoB of K. variicola-positive isolates identified by multiplex-PCR support the correct identification and differentiation of K. variicola from K. pneumoniae clinical isolates.

Conclusions

This multiplex-PCR provides the means to reliably identify and genotype K. variicola. This tool could be very helpful for clinical, epidemiological, and population genetics studies of this species. A low but significant prevalence of K. variicola isolates was found, implying that misclassification had occurred previously. We believe that our multiplex-PCR assay could be of paramount importance to understand the population dynamics of K. variicola in both clinical and environmental settings.