Biology subjects

Hasegawa, M.

Publications and source records attributed to Hasegawa, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Occurrence and persistence of pseudo-tail spots in the barn swallow

While numerous studies have confirmed sexual selection for ornamental traits in animals, it remains unclear about how animals exaggerate ornamentation beyond their original traits. I found that some Asian barn swallows Hirundo rustica gutturalis possessed pseudo-tail spots in their undertail coverts. A close inspection showed its remarkable resemblance to the white tail spots, a well-known sexual signal in this species, although pseudo-tail spots in the undertail covers do not incur any flight cost, unlike the white tail spots on the tail itself. Presence of pseudo-tail spots can thus represent an initial stage of a deceptive elaboration as predicted by sexual selection theory. The frequency of pseudo-tail spots in the study population remained low even a decade after the first observation (ca. 7%), but was higher compared to other populations (e.g., 1% in another Japanese population). The slow progress of evolution, perhaps due to the low detectability of the trait, provides a unique opportunity to observe contemporary evolution of ornament exaggeration across traits.

evolutionary biology↗

bioRxiv2024

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

bioRxiv2023

Maneuverable flight evolved with forked tails and opportunities for extrapair mating in swallows and martins (Aves: Hirundininae)

Whole-organism performance in relation to ornamentation is often examined to evaluate the cost of ornamentation, assuming that high performance is favored by viability selection. These studies typically conduct experimental manipulations of ornamentation, which potentially impair phenotypic integration with compensatory traits, making it difficult to clarify performance function of ornamentation. Here, we adopted an alternative approach, macroevolutionary analysis, and examined the flight performance of swallows (Aves: Hirundininae) in relation to tail fork depth to clarify evolutionary force favoring the ornamentation. We found that a measure of flight performance, presence of notable non-straight flight including maneuvering, turning, and swerving, peaked at intermediate fork depth, which appear to support viability selection for moderately forked tails. However, the quadratic relationship was found only in males, and hirundines with high opportunities for extrapair mating had higher probability of non-straight flight, indicating the importance of sexual selection. The current findings indicate that the flight performance of hirundines evolved through sexual selection, at least partially; thus, its relationship with forked tail might not clarify the viability cost of ornamentation. Whole-organism performance should be carefully interpreted when deducing the cost function, and thus, the evolutionary driver, of ornamentation.

evolutionary biology↗

bioRxiv2023

A procedure for solid phase extractions using metal oxide coated silica column in lipidomics

Lipid enrichment is indispensable for enhancing the coverage of targeted molecules in mass spectrometry (MS)-based lipidomics studies. In this study, we developed a simple stepwise fractionation method using a titanium- and zirconium-dioxide-coated solid-phase extraction (SPE) silica column that separates neutral lipids, phospholipids, and other lipids, including fatty acids (FAs) and glycolipids. Chloroform was used to dissolve the lipids, and neutral lipids, including steryl esters and di- and triacylglycerols, were collected in the loading fraction. Second, methanol with formic acid (99:1, v/v) was used to retrieve FAs, ceramides, and glycolipids, including glycosylated ceramides and glycosylated diacylglycerols, by competing for affinity with the Lewis acid sites on the metal oxide surface. Finally, phospholipids strongly retained via chemoaffinity interactions were eluted using a solution containing 5% ammonia and high water content (45:50 v/v, 2-propanol:water), which canceled the electrostatic and chelating interactions with the SPE column. High average reproducibility of <10% and coverage of [~]100% compared to those of the non-SPE samples were demonstrated by untargeted lipidomics of human plasma and mouse brain, testis, and feces. The advantage of our procedure was showcased by characterizing minor lipid subclasses, including dihexosylceramides containing very long-chain polyunsaturated FA in the testis, mono- and digalactosyl monoacylglycerols in feces, and acetylated and glycolylated derivatives of gangliosides in the brain that were not detected using conventional solvent extraction methods. Likewise, the value of our method in biology is maximized during glycolipidome profiling in the absence of neutral lipids and phospholipids that cover more than 80% of the chromatographic peaks. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/562428v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@170b451org.highwire.dtl.DTLVardef@4e4d3forg.highwire.dtl.DTLVardef@b1a1d4org.highwire.dtl.DTLVardef@1f77b31_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Using data-dependent and independent hybrid acquisitions for fast liquid chromatography-based untargeted lipidomics

Untargeted lipidomics using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has become an essential technique for large cohort studies. When a fast LC gradient of less than 10 min is used for the rapid screening of lipids, the annotation rate decreases because of the lower coverage of the MS/MS spectra caused by the narrow peak width. We propose a systematic procedure to achieve a high annotation rate in fast LC-based untargeted lipidomics by integrating data-dependent acquisition (DDA), and sequential window acquisition of all theoretical mass spectra data-independent acquisition (SWATH-DIA) techniques with the updated MS-DIAL program. Our strategy uses variable SWATH-DIA methods for quality control (QC) samples, which are a mixture of biological samples analyzed multiple times to correct MS signal drifts. In contrast, biological samples are analyzed using DDA to facilitate the structural elucidation of lipids using the pure spectrum to the maximum extent. We demonstrate our workflow using an 8.6 min LC gradient, where QCs are analyzed using five different SWATH-DIA methods. The results indicated that using both DDA and SWATH-DIA achieves 2.0-fold annotation coverage from publicly available benchmark data obtained by a fast LC-DDA-MS technique and offers 94.5% lipid coverage compared with the benchmark dataset from a 25 min LC gradient. Our study demonstrated that harmonized improvements in the analytical conditions and informatics tools provide a comprehensive lipidome in fast LC-based untargeted lipidomics, not only for large-scale studies but also for small-scale experiments, contributing to both clinical applications and basic biology.

bioinformatics↗

bioRxiv2023

Network state changes in sensory thalamus represent learned outcomes.

Thalamic brain areas play an important role in adaptive behaviors. Nevertheless, the population dynamics of thalamic relays during learning across sensory modalities remain mostly unknown. Using a cross-modal sensory reversal learning paradigm combined with deep brain two-photon calcium imaging of large populations of auditory thalamus (MGB) neurons, we identified that MGB neurons are biased towards reward predictors independent of modality. Additionally, functional classes of MGB neurons aligned with distinct task periods and behavioral outcomes, both dependent and independent of sensory modality. During non-sensory delay periods, MGB ensembles developed coherent neuronal representation as well as distinct co-activity network states reflecting predicted task outcome. These results demonstrate flexible cross-modal ensemble coding in auditory thalamus during adaptive learning and highlight its importance in brain-wide cross-modal computations during complex behavior. SummaryDeep brain imaging reveals flexible network states of sensory thalamus predicting task outcome in mice.

neuroscience↗

bioRxiv2023

Sexually dimorphic leading-edge serrations evolved in silent swallows

Leading-edge serrations are specialized feather structures, mitigating acoustic noise during foraging flight in owls, and have been extensively studied and applied to man-made noise-reducing structures. Similar structures occur in swallows, although the ecological functions of the serrations in these species remain unclear. I conducted macroevolutionary analyses of hirundines (Aves: Hirundininae), in which leading-edge serrations have evolved multiple times, to examine their evolution in relation to ecological context. I found that silent hirundines showed a higher probability of possessing leading-edge serrations, indicating that leading-edge serrations of swallows have an acoustic function as in owls. However, the probability of possessing leading-edge serrations had no detectable association with prey type in hirundines, indicating that their acoustic functions would evolve independent of foraging adaptation in this clade. Instead, the presence of leading-edge serrations was positively associated with relative testes mass, a well-known index of sperm competition, in hirundines. These findings explain sexually dimorphic expression of leading-edge serrations, a unique characteristic in this clade. In contrast to owls, in which serrations are considered an adaptation for silent foraging, sperm competition would favor the evolution of leading-edge serrations in hirundines, which illustrates that totally different selection pressures favor homologous traits in two taxa.

evolutionary biology↗

bioRxiv2023

Reduced ornamentation became elaborated in benign environments in a bird species

Many empirical studies have focused on highly-ornamented species to identify ecological factors that maintain the ornamentation or favour its exaggeration. By contrast, although reduction or loss of ornamentation appears to be widespread, species with reduced/lost ornamentation and its relationship with ecological factors are rarely focused on. Here, based on data collected over four years, we studied outermost tail feather length, i.e. a well-known sexual ornamentation in this clade, in relation to roosting location in the Pacific swallow Hirundo tahitica during winter. In contrast to congeners, this species has inconspicuous tail ornamentation, i.e. very shallowly forked tails with vestigial streamers, providing a rare opportunity to study the ecological factors driving reduced ornamentation. We found that Pacific swallows mainly roost in old nests under bridges over rivers, which resemble their original roosting sites, but some roost in old nests under the eaves of houses above the ground. Individuals roosting under the eaves of houses had significantly longer outermost (but not central) tail feathers than those roosting under bridges. Individuals roosting under the eaves of houses were heavier and showed lower physiological stress, and thus might better endure the maintenance cost, favouring ornament elaboration. Because we controlled for the effects of sex and age, these factors would not confound the observed pattern. Reduced ornamentation, as found in Pacific swallows roosting under their original roosting sites, could become elaborated in benign environments (i.e., under eaves, here), stressing the importance of balance between the costs and benefits of ornamentation.

ecology↗

bioRxiv2023

UV-induced feather color change reflects its porphyrin content

Pigmentary coloration is widespread in animals. Its evolutionary and ecological features are often attributed to the property of predominant pigments; therefore, most research has focused on predominant pigments such as carotenoids in carotenoid-based coloration. However, coloration results from predominant pigments and many other minority pigments, and the importance of the latter is overlooked. Here, we focused on porphyrin, an "uncommon" pigment found in bird feathers, and investigate its importance in the context of feather color changes in the barn swallow Hirundo rustica. We found that the "pheomelanin-based coloration" of the barn swallow faded after the irradiation of UV light, and this effect was particularly strong in the feathers of young swallows (nestlings and fledglings, here). We also found that it is not the predominant pigment, pheomelanin, but protoporphyrin IX pigment that showed the same pattern of depigmentation after the irradiation of UV light, particularly in the feathers of young swallows. In fact, the abovementioned age-dependent feather color change was statistically explained by the amount of porphyrin in the feathers. The current study demonstrates that a minority pigment, porphyrin, explains within-season dynamic color change, an ecological feature of feather coloration. The porphyrin-mediated rapid color change would benefit young birds, in which feather coloration affects the parental food allocation during a few weeks before independence, but not later. Future studies should not ignore these minor but essential pigments and their evolutionary and ecological functions. Significance statementPredominant pigments are assumed to determine animal coloration and its ecological features. It is then not surprising that the evolutionary and ecological features of animal coloration are often attributed to the chemical properties of predominant pigments. However, coloration results from predominant pigments and several other minority pigments. By irradiating UV light on reddish throat feathers of the barn swallow Hirundo rustica, we examined within-season dynamic color change in relation to a minority pigment, porphyrin, which has not previously been examined but is a candidate pigment for feather color change, because porphyrin can be easily photodegraded. We found that not the predominant pigment, pheomelanin, but porphyrin pigments explained the feather color change. Minor pigments and their chemical properties should not be dismissed to understand the ecological and evolutionary functions of animal coloration.

zoology↗

bioRxiv2023

Tau Filaments from Amyotrophic Lateral Sclerosis/Parkinsonism-Dementia Complex (ALS/PDC) adopt the CTE Fold

The amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterised by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here we used electron cryo-microscopy (cryo-EM) to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in two Kii cases. We also identified a novel Type III CTE tau filament, where protofilaments pack against each other in an anti-parallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors. SIGNIFICANCEA neurodegenerative disease of unknown cause on the island of Guam and the Kii peninsula of Japan has been widely studied, because patients can suffer from the combined symptoms of motor neuron disease, parkinsonism and dementia. Abnormal filamentous inclusions made of tau protein characterise this amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) and their formation closely correlates with neurodegeneration. Here we have used electron cryo-microscopy (cryo-EM) to show that tau filaments from ALS/PDC are identical to those from chronic traumatic encephalopathy (CTE), a disease caused by repetitive head impacts or blast waves. CTE tau filaments are also found in subacute sclerosing panencephalitis, which is a rare consequence of measles infection. ALS/PDC may therefore also be caused by environmental factors.

neuroscience↗

bioRxiv2023

Cryo-EM structures of tau filaments from SH-SY5Y cells seeded with brain extracts from cases of Alzheimer's disease and corticobasal degeneration

The formation of amyloid filaments through templated seeding is believed to underlie the propagation of pathology in most human neurodegenerative diseases. A widely used model system to study this process is to seed amyloid filament formation in cultured cells using human brain extracts. Here, we report the electron cryo-microscopy (cryo-EM) structures of tau filaments from undifferentiated seeded SH-SY5Y cells, that transiently expressed N-terminally HA-tagged 1N3R or 1N4R human tau, using brain extracts from individuals with AD or CBD. Although the resulting filament structures differed from those of the brain seeds, some degree of structural templating was observed. Studying templated seeding in cultured cells, and determining the structures of the resulting filaments, can thus provide insights into the cellular aspects underlying neurodegenerative diseases.

neuroscience↗

bioRxiv2023

Identical tau filaments in subacute sclerosing panencephalitis and chronic traumatic encephalopathy

Subacute sclerosing panencephalitis (SSPE) occurs in some individuals after measles infection, following a symptom-free period of several years. It resembles chronic traumatic encephalopathy (CTE), which happens after repetitive head impacts or exposure to blast waves, following a symptom-free period. As in CTE, when present, the neurofibrillary changes of SSPE are concentrated in superficial cortical layers. Here we used electron cryo-microscopy of tau filaments from two cases of SSPE to show that the tau folds of SSPE and CTE are identical. Two types of filaments were each made of two identical protofilaments with an extra density in the {beta}-helix region. Like in CTE, the vast majority of tau filaments were Type I, with a minority of Type II filaments. These findings suggest that the CTE tau fold can be caused by different environmental insults, which may be linked by inflammatory changes.

neuroscience↗

bioRxiv2022

Macroevolutionary analysis of swallows revived the sight-line hypothesis

The evolution of conspicuous ornamentation is often thought to be the consequence of sexual selection, but this might not always be the case. One such candidate is contrasting pale-dark facial color patterns in front of eyes in insectivorous birds and other animals (lore-forehead borderlines, hereafter). A sight-line hypothesis suggested that the contrasting color between lore and forehead assists in tracking and capturing a fast-moving prey. However, this classic hypothesis have been criticized (and thus ignored) for several reasons including lack of formal statistical test controlling for phylogenetic inertia and confounding effect of dark facial color markings that are beneficial by reducing glare. Here, using a phylogenetic comparative approach, we tested the sight-line hypothesis and a widespread alternative explanation, the sexual selection hypothesis, in hirundines (Aves: Hirundinidae). We found no support for the sexual function of lore-forehead borderline in hirundines, because lore-forehead borderline was not positively related to indices of sexual selection (sexual plumage dimorphism and extrapair mating opportunity). In contrast, we found consistent support for the sight-line hypothesis. Species foraging on large prey items (i.e., fast prey) had higher degrees of lore-forehead borderline than others in this clade. Furthermore, an analysis of evolutionary pathways suggested inter-dependent evolution of lore-forehead borderline and prey size; transitions to the state with large prey and no lore-forehead borderline were less likely to occur than transitions from that state. These results remained significant when excluding species that lack dark lore, and thus, not mere presence of dark lores, but contrasting color patterns would be important. To my knowledge, the current study is the first macroevolutionary support for the sight-line hypothesis.

evolutionary biology↗

bioRxiv2022

Coevolutionary maintenance of forked tails and song in hirundines (Aves: Hirundininae)

Both conspicuous plumage ornamentation and song are well-known examples of sexually selected traits but their interrelationship is not well-known, perhaps in part because of confounding factors, including interspecific variation in ecology, habitat, morphology, and type of ornamentation. Here, using a phylogenetic comparative approach, we examined the evolutionary relationship between forked tails and the presence/absence of song in hirundines (Aves: Hirundininae). Hirundines have similar ecology (e.g., aerial insectivores, social monogamy, and biparental provisioning), morphology (e.g., syrinx with nearly complete bronchial rings), and plumage ornamentation (i.e., a sexually selected forked tail), which provides a unique opportunity to examine the evolutionary associations between plumage ornamentation and song. In particular, hirundines have repeatedly lost their ornamentation, forked tails, enabling us to test their association with the evolutionary gain/loss of their simple song. After controlling for phylogeny and covariates, we demonstrated that song was less likely to be found in species with forkless tails than in species with forked tails. Two correlates of tail shape, sexual dimorphism in the overall plumage characteristics as a well-known measure of sexual selection and incubation type as a measure of extrapair mating opportunity, had no detectable relationship with the presence/absence of song, indicating the importance of forked tails, rather than their correlates. Evolutionary pathway analysis further supported the correlated evolution of the two traits, in which forked tails and song are maintained together and less likely to be lost under the presence of each other. The current study provided macroevolutionary support for the integrated use of visual and acoustic courtship traits.

evolutionary biology↗

bioRxiv2022

Energy transfer in ubiquitous rhodopsin pumps with xanthophyll antennas

Energy transfer from light-harvesting ketocarotenoids to light-driven proton pumps xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium1 and a terrestrial cyanobacterium2. Attempts to find carotenoids that bind and transfer energy to rhodopsin proton pumps from the abundant marine and freshwater photoheterotrophs have thus far failed3-5. Here, using functional metagenomics combined with chromophore extraction from the environment, we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet/blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas have a significant impact on rhodopsin phototrophy in the worlds lakes, seas and oceans.

microbiology↗

bioRxiv2022

Cryo-EM structures of α-synuclein filaments from Parkinson's disease and dementia with Lewy bodies

Parkinsons disease (PD) is the most common movement disorder, with resting tremor, rigidity, bradykinesia and postural instability being major symptoms (1). Neuropathologically, it is characterised by the presence of abundant filamentous inclusions of -synuclein in the form of Lewy bodies and Lewy neurites in some brain cells, including dopaminergic nerve cells of the substantia nigra (2). PD is increasingly recognised as a multisystem disorder, with cognitive decline being one of its most common non-motor symptoms. Many patients with PD develop dementia more than 10 years after diagnosis (3). PD dementia (PDD) is clinically and neuropathologically similar to dementia with Lewy bodies (DLB), which is diagnosed when cognitive impairment precedes parkinsonian motor signs or begins within one year from their onset (4). In PDD, cognitive impairment develops in the setting of well-established PD. Besides PD and DLB, multiple system atrophy (MSA) is the third major synucleinopathy (5). It is characterised by the presence of abundant filamentous -synuclein inclusions in brain cells, especially oligodendrocytes (Papp-Lantos bodies). We previously reported the electron cryo-microscopy (cryo-EM) structures of two types of -synuclein filaments extracted from the brains of individuals with MSA (6). Each filament type is made of two different protofilaments. Here we report that the cryo-EM structures of -synuclein filaments from the brains of individuals with PD, PDD and DLB are made of a single protofilament (Lewy fold) that is markedly different from the protofilaments of MSA. These findings establish the existence of distinct molecular conformers of assembled -synuclein in neurodegenerative disease.

neuroscience↗

bioRxiv2022

High salt induces cognitive impairment via the angiotensin II-AT1 and prostaglandin E2-EP1 systems

High salt (HS) intake is a known risk factor for hypertension and dementia. Clinical studies have shown that antihypertensive drugs can decrease the incidence of dementia. Accordingly, a strong relationship can be suggested between hypertension and cognitive impairment. It is well-known that angiotensin II (Ang II)-AT1 and prostaglandin E2 (PGE2)-EP1 systems are involved in hypertension and neurotoxicity. However, the involvement of these systems in HS-mediated hypertension and emotional and cognitive impairments remains unclear. Herein, we demonstrated that hypertension and impaired social behavior and object recognition memory following HS intake could be associated with tau hyperphosphorylation, decreased phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII), and postsynaptic density protein 95 (PSD95) expression in the prefrontal cortex and hippocampus of mice. These changes were blocked by pharmacological treatment with losartan, an Ang II receptor blocker (ARB), or EP1 gene knockout. Our findings suggest that Ang II-AT1 and PGE2-EP1 systems could be novel therapeutic targets for hypertension-induced dementia.

neuroscience↗

bioRxiv2022

Male mate preference against tail-elongated females in the barn swallow

The function of female ornamentation in the context of (inter)sexual selection attracts keen attention these days, but empirical field studies are mostly based on indirect measures such as mating patterns; direct evidence of male mate preference on female ornamentation while controlling for confounding factors is needed. Here we performed model presentation experiments to study male mate preference in the barn swallow Hirundo rustica, a model species of sexual selection. Female barn swallows have somewhat shorter tails than males, but their tails are still long and costly. Although many correlational and experimental studies of live females have focused on long tails in female barn swallows over the last three decades, direct behavioral tests of male mate preference are lacking. By using a sequential model presentation experiment, in which we repeated the trials with the same males, we found that males significantly reduced the number of pairing displays when they were presented with tail-elongated female models compared to control female models. Interaction between treatment and male tail length was far from significant. The observed pattern is inconsistent with the prevailing view that costly female ornamentation is maintained via male preference for more ornamented females. Rather, the observed pattern is consistent with the sexual mimicry hypothesis, in which females can avoid sexual (and social) harassment by mimicking males.

animal behavior and cognition↗