Biology subjects

Boyko, A.

Publications and source records attributed to Boyko, A..

7 recordsLinked to original sources

bioRxiv2026

Sex-related differences in healthy aging: changes in neuroelectric brain activity reconstructed from resting-state MEG

Sex-related differences in the aging of the human brain were studied using large array of experimental data. The open archive CamCan was used as a source of data: the magnetic encephalograms, co-registered with magnetic resonance images of the head, were obtained for each of 434 subjects (ages 18-87 years, mean age 54.7 {+/-}18.4): 217 females (ages 18-87 years, mean age 54.5 {+/-}18.4) and 217 males (ages 18-84 years, mean age 54.8 {+/-}18.3). Recordings were split in 10-year age cohorts, each cohort consisted of equal number of men and women to calculate average intersex characteristics correctly. By massively solving the inverse problem, functional tomograms were calculated - the spatial distribution of elementary spectral components. Physiological noise was eliminated by joint analysis of MEG-based functional tomogram and magnetic resonance image for each subject. Then multichannel spectra were transformed into time series of the power of elementary current dipoles. Summary electric powers were calculated in six conventional frequency bands (1-4 Hz - delta; 4-8 Hz - theta; 8-13 Hz - alpha; 13-21 Hz - beta1; 21-30 Hz - beta2; 30-48 Hz - gamma), and sex differences in age-related changes were examined. It was found that in the youngest age cohort (18-29 years) the summary electrical power of the brain for males is 1.5 times greater than such power for females. For adults (30-69 years), male and female powers are approximately equal, while in older cohorts (70-87 years), male total brain power is greater. Age dependencies in various frequency bands are generally different for men and women, excluding higher frequencies 21-48 Hz. Basic conclusion can be made that after intersex averaging total electric power of the human brain is invariant through the lifespan from 18 to 87 years. The proposed method of joint MEG and MRI analysis can be used for further study of the sex-related details of brain sources in their connection with age changes.

neuroscience↗

bioRxiv2024

Total neuroelectric brain activity derived from resting-state MEG is invariable across the adult lifespan

Ageing of the human brain was studied using large array of experimental data. The magnetic encephalograms and magnetic resonance images of the head were obtained from the open archive CamCAN. Bad data were rejected, then functional tomograms were found - the spatial distribution of elementary spectral components. Physiological noise was eliminated by joint analysis of the functional tomograms and magnetic resonance images. By massively solving the inverse problem, multichannel spectra were transformed into time series of the power of elementary current dipoles. Age-related changes in the electrical power of various brain rhythms were examined. It was found that the summary electrical activity of the brain is constant throughout a persons life. The electric power is redistributed during the lifetime: delta rhythm is diminishing, giving slow rise to all other rhythms.

neuroscience↗

bioRxiv2024

The chemoreceptor controlling the Wsp-like transduction pathway in Halomonas titanicae KHS3 binds purine derivatives

The chemosensory pathway HtChe2 from the marine bacterium Halomonas titanicae KHS3 controls the activity of a diguanylate cyclase. Constitutive activation of the pathway results in colony morphology alterations and increased ability to form biofilm. Such characteristics resemble the behaviour of the Wsp pathway of Pseudomonas. In this work we investigate the specificity of Htc10, the only chemoreceptor coded within the HtChe2 gene cluster. Thermal shift analyses performed with the Htc10 ligand-binding domain led to the identification of purine derivatives as ligands. This ligand-binding domain was crystallized in the presence of guanine or hypoxanthine and its structure was solved by X-ray protein crystallography. The sensor domain adopts a double-cache folding, with ligands bound to the membrane-distal pocket. A high-resolution structure of the occupied guanine-binding pocket allowed the identification of the involved residues. These residues were validated by site directed mutagenesis and thermal shift or isothermal calorimetry analyses of the protein variants. The dissociation constants for guanine or hypoxanthine of the intact domain were in the low micromolar range. To our knowledge, this is the first description of binding specificity for a chemoreceptor that controls the activity of an associated diguanylate cyclase, and opens the way for dynamic studies of the signalling behaviour of this kind of sensory complex. A comparison between Htc10 and the functionally equivalent WspA receptor from Pseudomonas revealed no significant sequence similarities. In contrast, highly conserved Htc10-like receptors were found in distant bacteria carrying HtChe2-like clusters.

microbiology↗

bioRxiv2023

High resolution cryo-EM and crystallographic snapshots of the large actinobacterial 2-oxoglutarate dehydrogenase: an all-in-one fusion with unique properties

Actinobacteria possess unique ways to regulate the oxoglutarate node located in the central position of the tricarboxylic acid cycle, a crossroad between energy conservation and nitrogen metabolism. Here, we studied the decarboxylative oxidation route that leads, through the 2-oxoglutarate dehydrogenase (ODH) complex, to the generation of succinyl-CoA and reduced equivalents to feed the respiratory chain. Compared to most organisms in which the oxidative decarboxylation and reductive acylation steps are carried out by different enzymes within the ODH complex, actinobacteria rely on an all-in-one protein (OdhA) in which both activities are carried out by the same polypeptide. We describe high-resolution cryo-EM and X-ray crystallography snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that folds into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the FHA (Fork-Head Associated) signalling protein OdhI, delivering new molecular details on how this actinobacterial-specific switching mechanism operates. Overall, the quaternary organization of OdhA represents a new piece of the fascinating puzzle of the synergistic, mixed pyruvate dehydrogenase/2-oxoglutarate dehydrogenase actinobacterial supercomplex.

biochemistry↗

bioRxiv2021

Complex feline disease mapping using a dense genotyping array

The current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.

genetics↗

bioRxiv2020

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3 end of LINE-1_Cfs (i.e., LINE-1_Cf 3-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation. SignificanceAdvancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.

genomics↗

bioRxiv2019

Inbreeding depression causes reduced fecundity in Golden Retrievers

Inbreeding depression has been demonstrated to impact vital rates, productivity, and performance in many domestic species. Many in the field have demonstrated the value of genomic measures of inbreeding compared to pedigree-based estimates of inbreeding; further, standardized, high-quality phenotype data on all individuals is invaluable for longitudinal analyses of a study cohort. We compared measures of reproductive fitness in a small cohort of Golden Retrievers enrolled in the Golden Retriever Lifetime Study (GRLS) to a genomic measurement of inbreeding, FROH. We demonstrate a statistically significant negative correlation between fecundity and FROH.This work sets the stage for larger scale analyses to investigate genomic regions associated with fecundity and other measures of fitness.

genomics↗