Population structure and gene flow of the syntopic turtles Emys and Mauremys from coastal and inland regions of Anatolia (Turkey): results from mitochondrial and microsatellite data

Revealing the genetic basis of the existence of different species living together in different geographic regions provides clarification of this phylogeographic differentiation. In this study, we investigated the population genetics and evaluated the level of genetic variation of inland and coastal populations of Mauremys and Emys in Turkey. Tissue samples of 196 terrapins were studied which were collected from syntopic coastal (Gölbent-Söke/Ayd?n; M. rivulata and E. orbicularis) and inland populations (Bahçesaray/Aksaray; M. caspica and E. orbicularis). DNA was isolated using the InnuPREP DNA Mini Kit. Mitochondrial DNA sequences and allelic variation at 13 microsatellite loci for Mauremys and 12 microsatellite loci for Emys were examined.  Three haplotypes were found for Emys orbicularis (Im, Ip and Iw) collected from the coastal region and two haplotypes for Emys orbicularis (Ig and Im) collected from inland. Two haplotypes were identified for M. caspica (Cmt8 and Cmt9) and three haplotypes were identified for M. rivulata (Rmt3, Rmt24 and Rmt26). Using microsatellites and the software STRUCTURE the most probable value for K was revealed as two 2 for both species. The F_ST value between M. rivulata and M. caspica was 0.39, and between the coastal and inland populations of E. orbicularis 0.09. It can be concluded that Emys populations tend to evolve by somehow preserving the allelic richness they have and Mauremys populations continue to differentiate so that new species emerge in the evolutionary process to reach the ideal allelic structure.

     

Shorter leukocyte telomere length is associated with severity of COVID-19 infection.

The infection by COVID-19 is a serious global public health problem. An efficient way to improve this disease's clinical management would be to characterize patients at higher risk of progressing to critically severe infection using prognostic biomarkers. The telomere length could be used for this purpose. Telomeres are responsible for controlling the number of maximum cell divisions. The telomere length is a biomarker of aging and several diseases. We aimed to compare leukocyte telomere length (LTL) between patients without COVID-19 and patients with different clinical severity of the infection. Were included 53 patients who underwent SARS-CoV-2 PCR divided in four groups. The first group was composed by patients with a negative diagnosis for COVID-19 (n = 12). The other three groups consisted of patients with a confirmed diagnosis of COVID-19 divided according to the severity of the disease: mild (n = 15), moderate (n = 17) and severe (n = 9). The LTL was determined by Q-PCR. The severe group had the shortest LTL, followed by the moderate group. The negative and mild groups showed no differences. There is an increase of patients with hypertension (p = 0.0099) and diabetes (p = 0.0067) in moderate and severe groups. Severe group was composed by older patients in comparison with the other three groups (p = 0.0083). Regarding sex, there was no significant difference between groups (p = 0.6279). In an ordinal regression model, only LTL and diabetes were significantly associated with disease severity. Shorter telomere length was significantly associated with the severity of COVID-19 infection, which can be useful as a biomarker or to better understand the SARS-CoV-2 pathophysiology.     

Genetic diversity and geographic differentiation in the alternative legume Tripodion tetraphyllum (L.) Fourr. in North African populations

Wild legumes constitute an important component of widespread pastures in the Mediterranean basin. This region is experiencing remarkable effects from climate change, and continuous monitoring of species and population dynamics is important in order to plan and enact valuable conservation programmes. Tripodion tetraphyllum (L.) Fourr. [=Anthyllis tetraphylla L.] (2n=16), belongs to the tribe Loteae (Fabaceae), and could be very important for soil protection and sward improvement in abandoned or degraded Mediterranean areas. This alternative pasture legume is very closely related to Lotus japonicus and has some important characteristics for survival of the species in difficult and overgrazed Mediterranean areas. In this study, we have investigated the molecular diversity and population structure of T. tetraphyllum from North Africa using ISSR markers and plastidial microsatellites. To date, this is the first study concerning the genetic diversity and geographic differentiation of T. tetraphyllum. Ninety genotypes from three North African countries were analysed according to ISSRs, cpSSRs and one phenotypic trait. T. tetraphyllum shows a clear geographical structure, with differentiation associated with longitudinal differences; moreover, there is a general reduction in genetic diversity from Morocco to Tunisia. With all the markers used, strong differentiation was seen among collection sites. Our data highlight a genetic diversity gradient and cline of distribution, indicating that T. tetraphyllum has extended its area of distribution from Morocco to Tunisia.     

Enhanced Sensitivity of Surface Plasmon Resonance Phase-Interrogation Biosensor by Using Silver Nanoparticles

It is demonstrated that the sensitivity of surface plasmon resonance phase-interrogation biosensor can be enhanced by using silver nanoparticles. Silver nanoparticles were fabricated on silver films by using thermal evaporation. Sizes of silver nanoparticles on silver thin film can be tuned by controlling the deposition parameters of thermal evaporation. By using surface plasmon resonance heterodyne interferometey to measure the phase difference between the p and s polarization of incident light, we have demonstrated that sensitivity of glucose detection down to the order of 10⁻⁸ refractive index units can be obtained.     

Assessing forest products usage and local residents' perception of environmental changes in peri-urban and rural mangroves of Cameroon,Central Africa

Background

Deforestation is one of the most ubiquitous forms of land degradation worldwide. Although remote sensing and aerial photographs can supply valuable information on land/use cover changes, they may not regularly be available for some tropical coasts (e.g., Cameroon estuary) where cloud cover is frequent. With respect to mangroves, researchers are now employing local knowledge as an alternative means of understanding forest disturbances. This paper was primarily aimed at assessing the mangrove forest products usage, along with the local people's perceptions on environmental changes, between Littoral (Cameroon estuary) and Southern (mouth of the Nyong River and Mpalla village) regions of Cameroon.

Methods

The data from both locations were obtained through conducting household interviews and field observations.

Results

In the Cameroon estuary (Littoral region), 69.23% of respondents (mostly elders) could distinguish two to four mangrove plants, whereas the informants (65.45%) in the mouth of the Nyong River and Mpalla village (mostly young people interviewed from the Southern region) are familiar with only one or two commonly found mangroves. Also, more respondents from the Cameroon estuary are depending on mangroves for fuelwood (Rhizophora spp.) and housing (Rhizophora spp., Avicennia germinans (L.) Stearn and Nypa fruticans (Thumb.) Wurmb.) purposes, in contrast to Nyong River mouth and Mpalla village. Although local people perceived wood extraction as a greater disruptive factor, there are several causes for mangrove depletion in the Cameroon estuary. Among others, over-harvesting, clear-felled corridors, sand extraction and housing were found important. Furthermore, a decline in mangrove fauna composition (in terms of fishery products) was recorded in the Littoral as well as Southern regions. However, the causes of such perceived negative changes were not similar in both cases.

Conclusions

Findings of this study highlight the need to improve sustainable management of the mangrove ecosystems through afforestation (in large impacted areas), selective removal of senescent tree stems and branches (in little damage stands), regulating sand extraction and housing activities, and creating awareness and law enforcement.

     

Arabidopsis MSI1 connects LHP1 to PRC2 complexes

Polycomb group (PcG) proteins form essential epigenetic memory systems for controlling gene expression during development in plants and animals. However, the mechanism of plant PcG protein functions remains poorly understood. Here, we probed the composition and function of plant Polycomb repressive complex 2 (PRC2). This work established the fact that all known plant PRC2 complexes contain MSI1, a homologue of Drosophila p55. While p55 is not essential for the in vitro enzymatic activity of PRC2, plant MSI1 was required for the functions of the EMBRYONIC FLOWER and the VERNALIZATION PRC2 complexes including trimethylation of histone H3 Lys27 (H3K27) at the target chromatin, as well as gene repression and establishment of competence to flower. We found that MSI1 serves to link PRC2 to LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), a protein that binds H3K27me3 in vitro and in vivo and is required for a functional plant PcG system. The LHP1–MSI1 interaction forms a positive feedback loop to recruit PRC2 to chromatin that carries H3K27me3. Consequently, this can provide a mechanism for the faithful inheritance of local epigenetic information through replication.     

European Phaseolus coccineus L. landraces: Population Structure and Adaptation,as Revealed by cpSSRs and Phenotypic Analyses

Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.     

Nucleotide diversity of a genomic sequence similar to <Emphasis Type="Italic">SHATTERPROOF</Emphasis> (<Emphasis Type="Italic">PvSHP1</Emphasis>) in domesticated and wild common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Evolutionary studies in plant and animal breeding are aimed at understanding the structure and organization of genetic variations of species. We have identified and characterized a genomic sequence in Phaseolus vulgaris of 1,200 bp (PvSHP1) that is homologous to SHATTERPROOF-1 (SHP1), a gene involved in control of fruit shattering in Arabidopsis thaliana. The PvSHP1 fragment was mapped to chromosome Pv06 in P. vulgaris and is linked to the flower and seed color gene V. Amplification of the PvSHP1 sequence from the most agronomically important legume species showed a high degree of interspecies diversity in the introns within the Phaseoleae, while the coding region was conserved across distant taxa. Sequencing of the PvSHP1 sequence in a sample of 91 wild and domesticated genotypes that span the geographic distribution of this species in the centers of origin showed that PvSHP1 is highly polymorphic and, therefore, particularly useful to further investigate the origin and domestication history of P. vulgaris. Our data confirm the gene pool structure seen in P. vulgaris along with independent domestication processes in the Andes and Mesoamerica; they provide additional evidence for a single domestication event in Mesoamerica. Moreover, our results support the Mesoamerican origin of this species. Finally, we have developed three indel-spanning markers that will be very useful for bean germplasm characterization, and particularly to trace the distribution of the domesticated Andean and Mesoamerican gene pools.