Specific binding of synthetic human pancreatic growth hormone releasing factor (1-40-OH) to bovine anterior pituitaries

We have studied the specific binding of a synthetic 40 amino acid, free carboxy terminus analog of human pancreatic growth hormone releasing factor (hp GRF-40-OH) to partially purified homogenates of bovine anterior pituitaries. The binding of hpGRF-40-OH to pituitary receptors at 4 degrees C reached maximal level in 4 hours and remained steady for the next 18 hours. Specific binding increased linearly with the amount of protein present in the assay. 125I-hpGRF-40-OH binding to pituitary homogenates was competitively inhibited by hpGRF-40-OH but not by unrelated hormones. The competition curve and Scatchard analysis suggest the presence of single class of receptors with a Kd congruent to 3nM and binding capacity of approximately 200 fmoles/mg protein. This is the first demonstration of specific receptors for GRF on anterior pituitary cells.     

Towards pan-genome read alignment to improve variation calling

Background

Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation.

Results

We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation – a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC.

Conclusions

Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.

     

Length‐weight analysis of three needlefish species from the Lakshadweep archipelago

Length‐weight relationships (LWRs) of three needlefishes belonging to the family Belonidae viz., Ablennes hians, Tylosurus crocodilus and Tylosurus acus melanotus were estimated based on samples exploited from a gill‐net fishery in Androth, an island in the Lakshadweep archipelago. The estimated allometric co‐efficient b value ranged from 3.047 (T. acus melanotus) to 3.274 (A. hians), and r² value ranged from 0.911 (T. acus melanotus) to 0.973 (A. hians). The first estimate of LWR for these three commercially exploited needlefish species from the Lakshadweep islands indicate local populations to be fairly robust and forms a basis for future management of fishing stock in the region.     

A safe and complete algorithm for metagenomic assembly

Background

Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bacterial species present in a sequencing sample. This problem can be naturally formulated as finding a collection of circular walks of a directed graph G that together cover all nodes, or edges, of G.

Approach

We address this problem with the “safe and complete” framework of Tomescu and Medvedev (Research in computational Molecular biology—20th annual conference, RECOMB 9649:152–163, 2016). An algorithm is called safe if it returns only those walks (also called safe) that appear as subwalk in all metagenomic assembly solutions for G. A safe algorithm is called complete if it returns all safe walks of G.

Results

We give graph-theoretic characterizations of the safe walks of G, and a safe and complete algorithm finding all safe walks of G. In the node-covering case, our algorithm runs in time \(O(m^2 + n^3)\), and in the edge-covering case it runs in time \(O(m^2n)\); n and m denote the number of nodes and edges, respectively, of G. This algorithm constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.

     

How common is ecological speciation in plant-feeding insects? A 'Higher' Nematinae perspective

Background  

Ecological speciation is a process in which a transiently resource-polymorphic species divides into two specialized sister lineages as a result of divergent selection pressures caused by the use of multiple niches or environments. Ecology-based speciation has been studied intensively in plant-feeding insects, in which both sympatric and allopatric shifts onto novel host plants could speed up diversification. However, while numerous examples of species pairs likely to have originated by resource shifts have been found, the overall importance of ecological speciation in relation to other, non-ecological speciation modes remains unknown. Here, we apply phylogenetic information on sawflies belonging to the 'Higher' Nematinae (Hymenoptera: Tenthredinidae) to infer the frequency of niche shifts in relation to speciation events.     

Fertile transgenic barley by particle bombardment of immature embryos

Transgenic, fertile barley (Hordeum vulgare L.) from the Finnish elite cultivar Kymppi was obtained by particle bombardment of immature embryos. Immature embryos were bombarded to the embryonic axis side and grown to plants without selection. Neomycin phosphotransferase II (NPTII) activity was screened in small plantlets. One out of a total of 227 plants expressed the transferred nptII gene. This plant has until now produced 98 fertile spikes (T₀), and four of the 90 T₀ spikes analyzed to date contained the nptII gene. These shoots were further analyzed and they expressed the transferred gene. From green grains, embryos were isolated and grown to plantlets (T₁). The four transgenic shoots of Toivo (the T₀ plant) produced 25 plantlets as T₁ progeny. Altogether fifteen of these T₁ plants carried the transferred nptII gene as detected with the PCR technique, fourteen of which expressed the nptII gene. The integration and inheritance of the transferred nptII gene was confirmed by Southern blot hybridization. Although present as several copies, the transferred gene was inherited as a single Mendelian locus into the T₂ progeny.     

Sex steroid hormone metabolism and prostate cancer

The growth and function of the prostate is dependent on androgens. The two predominant androgens are testosterone, which is formed in the testis from androstenedione and 5alpha-dihydrotestosterone, which is formed from testosterone by 5alpha-reductases and is the most active androgen in the prostate. Prostate cancer is one of the most common cancers among men and androgens are involved in controlling the growth of androgen-sensitive malignant prostatic cells. The endocrine therapy used to treat prostate cancer aims to eliminate androgenic activity from the prostatic tissue. Most prostate cancers are initially responsive to androgen withdrawal but become later refractory to the therapy and begin to grow androgen-independently. Using LNCaP prostate cancer cell line we have developed a cell model to study the progression of prostate cancer. In the model androgen-sensitive LNCaP cells are transformed in culture conditions into more aggressive, androgen-independent cells. The model was used to study androgen and estrogen metabolism during the transformation process. Our results indicate that substantial changes in androgen and estrogen metabolism occur in the cells during the process. A remarkable decrease in the oxidative 17beta-hydroxysteroid dehydrogenase activity was seen whereas the reductive activity seemed to increase. The changes suggest that during transformation estrogen influence is increasing in the cells. This is supported by the cDNA microarray screening results which showed over-expression of several genes up-regulated by estrogens in the LNCaP cells line representing progressive prostate cancer. Since local steroid metabolism controls the bioavailability of active steroid hormones in the prostate, the variations in steroid-metabolizing enzymes during cancer progression may be crucial in the regulation of the growth and function of the organ.     

Human familial and sporadic breast cancer: analysis of the coding regions of the 17β-hydroxysteroid dehydrogenase 2 gene (EDH17B2) using a single-strand conformation polymorphism assay

17-Hydroxysteroid dehydrogenase (17HSD) is one of the key enzymes in estrogen metabolism, catalyzing the reversible reaction between estradiol and the less active estrogen, estrone. The gene encoding this enzyme, EDH17B2, has been mapped to chromosome 17, region q12–q21, in the vicinity of BRCA1, an as yet unidentified gene that appears to be involved in familial breast cancer and in familial ovarian cancer. The possibility that EDH17B2 gene is the same as BRCA1 was tested by screening for mutations in the coding regions of EDH17B2, using a polymerase chain reaction/single-strand conformation polymorphism method. An AG transition creating a new BstUI site at exon 6 was the only frequent sequence alteration found in the coding region of the gene. This mutation also led to an amino acid substitution of serine to glycine at position 312 (312^S312^G) in the 17HSD protein. Since the nucleotide change was detected both in specimens from patients with familial or sporadic cancer and in control samples, and at similar rates, this mutation appears to be of a polymorphic nature. In addition, a rare polymorphism located at intron 5 was detected. This CT substitution creates a BbvI site and is not thought to have any effect on 17HSD activity. The results indicate that there are no major alterations in the coding areas of EDH17B2 and thus studies testing the hypothesis that EDH17B2 may be the same as BRCA1 should be extended to the promoter and regulatory elements of EDH17B2.     

Carbonate facies evolution from the late albian to Middle Cenomanian in Southern Istria (Croatia): influence of synsedimentary tectonics and extensive organic carbonate production

Summary During the Late Albian, Early and Middle Cenomanian in the NW part of the Adriatic Carbonate Platform (presentday Istria) specific depositional systems characterised by frequent lateral and vertical facies variations were established within a formerly homogeneous area, ranging from peritidal and barrier bars to the offshore-transition zone. In southern Istria this period is represented by the following succession: thin-bedded peritidal peloidal and stromatolitic limestones (Upper Albian); well-bedded foreshore to shoreface packstones/grainstones with synsedimentary dliding and slumping (Vraconian-lowermost Cenomanian); shoreface to off-shore storm-generated limestones (Lower Cenomanian); massive off-shore to shoreface carbonate sand bodies (Lower Cenomanian); prograding rudist bioclastic subaqueous dunes (Lower to Middle Cenomanian); rudist biostromes (Lower to Middle Cenomanian), and high-energy rudist and ostreid coquina beds within skeletal wackestones/packstones (Middle Cenomanian). Rapid changes of depositional systems near the Albian/Cenomanian transition in Istria are mainly the result of synsedimentary tectonics and the establishment of extensive rudist colonies producing enormous quantities of bioclastic material rather than the influence of eustatic changes. Tectonism is evidenced by the occurrence of sliding scars, slumps, small-scale synsedimentary faults and conspicuous bathymetric changes in formerly corresponding environments. Consequently, during the Early Cenomanian in the region of southern Istria, a deepening of the sedimentary environments occurred towards the SE, resulting in the establishment of a carbonate ramp system. Deeper parts of the ramp were below fair-weather wave base (FWWB), while the shallower parts were characterised by high-energy environments with extensive rudist colonies, and high organic production leading to the progradation of bioclastic subaqueous dunes. This resulted in numerous shallowing- and coarsening-upwards clinostratified sequences completely infilling formerly deeper environments, and the final re-establishment of the shallow-water environments over the entire area during the Middle Cenomanian.     

Genetic characterization of grey wolves (<Emphasis Type="Italic">Canis lupus</Emphasis> L. <Emphasis Type="Italic">1758</Emphasis>) from Bosnia and Herzegovina: implications for conservation

The grey wolves of Bosnia and Herzegovina form a subpopulation of the Dinaric-Balkan wolf population and represent one of Europe’s least studied wolf populations. Since the Dinaric-Balkan population is a valuable source of genetic diversity for neighboring populations, comprehensive assessments are warranted. We aimed to determine the genetic variability and structure of the grey wolf population from Bosnia and Herzegovina, as well as estimate levels of gene flow and inbreeding and evaluate genetic signals of a bottleneck. To do this, we analyzed the variability of eighteen microsatellite loci. We found moderately high genetic heterozygosity for wolves from Bosnia and Herzegovina, as described for other Dinaric-Balkan wolf populations. We reveal weak genetic structuring with two genetic clusters identified. Wolves from the eastern part of the region formed a relatively distinct cluster, whereas individuals in the second cluster overlapped quite considerably with admixed individuals. Despite the signal of genetic structure being weak, clustering of individuals from the eastern part of the country extended through all analyses. Thus, this cluster could be considered a separate management unit, perhaps requiring specific conservation attention.