Methylation of KvDMR1 involved in regulating the imprinting of CDKN1C gene in cattle

The CDKN1C gene encodes a cyclin‐dependent kinase inhibitor and is one of the key genes involved in the development of Beckwith–Wiedemann syndrome and cancer. In this study, using a direct sequencing approach based on a single nucleotide polymorphism (SNP) at genomic DNA and cDNA levels, we show that CDKN1C exhibits monoallelic expression in all seven studied organs (heart, liver, spleen, lung, kidney, muscle and subcutaneous fat) in cattle. To investigate how methylation regulates imprinting of CDKN1C in cattle, allele‐specific methylation patterns in two putative differential methylation regions (DMRs), the CDKN1C DMR and KvDMR1, were analyzed in three tissues (liver, spleen and lung) using bisulfite sequencing PCR. Our results show that in the CDKN1C DMR both parental alleles were unmethylated in all three analyzed tissues. In contrast, KvDMR1 was differentially methylated between the two parental alleles in the same tissues. Statistical analysis showed that there is a significant difference in the methylation level between the two parental alleles (P < 0.01), confirming that this region is the DMR of KvDMR1 and that it may be correlated with CDKN1C imprinting.     

Diversity measures in macroinvertebrate and zooplankton communities related to the trophic status of subtropical reservoirs: Contradictory or complementary responses?

Macroinvertebrate communities have been widely used as a tool for assessing the environmental quality of freshwater ecosystems, whereas zooplankton communities have been to some extent neglected. However, the importance of using different indicators to achieve a more comprehensive framework of assessment regarding water quality has been recognized. This study compared estimates of species richness (number of species) and the Shannon–Wiener index for data on macroinvertebrate and zooplankton communities in tropical reservoirs and related them to their trophic state. The trop+hic classification was obtained by applying the Carlson index (1977) modified by Toledo et al. (1983), and the index of the Brazilian Society of the Environmental Technology Agency. The comparative response of the different indicators was analyzed using a series of bivariate correlations (Draftsman’s plot). The results illustrate that diversity measures, namely species richness, responded differently when related to the trophic classification of reservoirs, depending on the community considered. The species richness of zooplankton was positively related to hypereutrophic conditions, due to the higher number of rotifer species, including tolerant generalist species and at the same time, as a result of the exclusion of species from other groups, whereas for macroinvertebrates, species richness was negatively related to hypereutrophic conditions. Melanoides tuberculatus, which exhibits a high tolerance and competitive ability under such conditions, was the dominant species in macroinvertebrate communities, which excluded endemic species and reduced local richness and diversity. The same indicators applied to the zooplankton and macroinvertebrate communities might therefore provide contradictory responses regarding ecological quality assessment in tropical reservoirs, which suggest that zooplankton should be taken into account among the biological quality elements considered in the ecological quality assessment, management, and restoration of water bodies.     

Planktonic indices in the evaluation of the ecological status and the trophic state of the longest lake in Poland

Due to the intensive mixing polymictic lakes should be homogenous. However, morphometric diversity and high water dynamics contribute to the differentiation of many parameters in various areas of the lakes. This study analyzes both phytoplankton and zooplankton to assess differences in water quality along the north–south axis of the longest lake in Poland. New phytoplankton indicators were applied for determining the lake's ecological status: the Q index based on functional groups and the PMPL (Phytoplankton Metric for Polish Lakes) index based on phytoplankton biomass. TSI_ROT index (Rotifer Trophic State Index), which comprises the percentage of species indicating a high trophic state in the indicatory group and the percentage of bacteriovorus in the Rotifera population, was used for zooplankton analysis.TP content was different at different sites – we observed its gradual increase from the south to the north. Spatial variation of phosphorus did not considerably affect plankton diversity. The phytoplankton was dominated by Oscillatoriales, typical of shallow, well-mixed eutrophic lakes. The ecological status of the lake based on the EQR (Ecological Quality Ratio) was poor or moderate. The zooplankton was dominated by rotifers (at almost all sites), which indicates a eutrophic state of the lake. The values of phytoplankton indices at the studied sites did not differ considerably; the differences resulted more from local conditions such as the contaminant inflow and the macrophyte development than water dynamics.We have demonstrated that in the lake dominated by filamentous Cyanobacteria the ecological status should be determined according to the PMPL index or other indices dependent on the dominant Cyanobacteria species. Since the Q index does not include the functional group S1, the results can lead to the false conclusion that water quality improves with an increased amount of phytoplankton. The high abundance of Cyanobacteria in the lake may have contributed to the poor growth of rotifers.     

Discovering Precise Temporal Patterns in Large-Scale Neural Recordings through Robust and Interpretable Time Warping

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Alternative rib bone biopsy measurements to estimate changes in skeletal mineral reserves in cattle

Rib bone biopsy samples are often used to estimate changes in skeletal mineral reserves in cattle but differences in sampling procedures and the bone measurements reported often make interpretation and comparisons among experiments difficult. ‘Full-core’ rib bone biopsy samples, which included the external cortical bone, internal cortical bone and trabecular bone (CB_ext, CB_int and Trab, respectively), were obtained from cattle known to be in phosphorus (P) adequate (P_adeq) or severely P-deficient (P_defic) status. Experiments 1 and 2 examined growing steers and Experiment 3 mature breeder cows. The thickness of cortical bone, specific gravity (SG), and the amount and concentration of ash and P per unit fresh bone volume, differed among CB_ext, CB_int and Trab bone. P concentration (mg/cc) was closely correlated with both SG and ash concentrations (pooled data, r=0.99). Thickness of external cortical bone (CBT_ext) was correlated with full-core P concentration (FC-P_conc) (pooled data, r=0.87). However, an index, the amount of P in CB_ext per unit surface area of CB_ext (PSACB; mg P/mm²), was more closely correlated with the FC-P_conc (pooled data, FC-P_conc=37.0+146×PSACB; n=42, r=0.94, RSD=7.7). Results for measured or estimated FC-P_conc in 10 published studies with cattle in various physiological states and expected to be P_adeq or in various degrees of P_defic status were collated and the ranges of FC-P_conc indicative of P adequacy and P deficiency for various classes of cattle were evaluated. FC-P_conc was generally in the range 130 to 170 and 100 to 120 mg/cc fresh bone in P_adeq mature cows and young growing cattle, respectively. In conclusion, the FC-P_conc could be estimated accurately from biopsy samples of CB_ext. This allows comparisons between studies where full-core or only CB_ext biopsy samples of rib bone have been obtained to estimate changes in the skeletal P status of cattle and facilitates evaluation of the P status of cattle.     

Genetic and allelopathic differences between populations of daisy fleabane Erigeron annuus (L.) Pers. (Asteraceae) from disturbed and stable habitats

The interactions between invasive plants and their habitats may vary at different phases of the invasion process and depend on the phenotypic plasticity or local adaptations of each species. In this study, we investigated whether habitat changes during the invasion process are related to variations in the physiological traits (allelopathic properties) and genetic differentiation of daisy fleabane (Erigeron annuus (L.) Pers.). E. annuus is a winter annual invasive species that originated in North America and is now distributed throughout Europe. Genetic and genotypic diversity analyses were performed for 37 populations of E. annuus based on inter simple sequence repeat (ISSR) polymorphisms. In total, 684 plants were analyzed; 342 were from stable habitats and 342 were from disturbed habitats. The genetic differences among the populations from the different habitats were studied using a Bayesian cluster analysis and an analysis of molecular variance (AMOVA) and by calculating the genetic and genotypic diversity parameters. A germination test using the juglone index was employed to examine the potential allelopathic properties of the plants from the different habitats. Bayesian cluster analysis, AMOVA and allelopathic effects evaluation revealed differences in the allelopathic potential and genetic structure of the E. annuus populations from the disturbed and stable habitats. This differentiation of populations could be associated with founder effects or with different selection pressures among habitats.     

Low mtDNA Cytb diversity and shallow population structure of Eleutheronema tetradactylum in the East China Sea and the South China Sea

Eleutheronema tetradactylum is an economically important fish species in China water. To investigate the genetic diversity and describe population structure of it, an 1151 base pair (bp) fragment of the mitochondrial DNA Cytb sequence was analyzed in 120 individuals from four populations in the East China Sea and the South China Sea. A total of 16 haplotypes were defined by 24 variable nucleotide sites. High level of haplotype diversity and low nucleotide diversity were observed in all populations. The results of AMOVA detected that 89.44% of the genetic variation occurred within populations. Significant genetic differentiations were detected among populations (0.05097, P < 0.05), but no large-scale regional differences were detected. Analysis of neutral evolution and mismatch distribution suggested no recent population expansion happened. The present results provided new information for genetic assessment, fishery management and conservation of this species.     

Finite time blow-up in some models of chemotaxis

We consider a class of models of chemotactic bacterial populations, introduced by Keller-Segel. For those models, we investigate the possibility of chemotactic collapse, in other words, the possibility that in finite time the population of predators aggregates to form a delta-function. To study this phenomenon, we construct self-similar solutions, which may or may not blow-up (in finite time), depending on the relative strength of three mechanisms in competition: (i) the chemotactic attraction of bacteria towards regions of high concentration in substrate (ii) the rate of consumption of the substrate by the bacteria and (iii) (possibly) the diffusion of bacteria. The solutions we construct are radially symmetric, and therefore have no relation with the classical traveling wave solutions. Our scaling can be justified by a dimensional analysis. We give some evidence of numerical stability.