Evolution of mitochondrial energy metabolism genes associated with hydrothermal vent adaption of Alvinocaridid shrimps

Most of Alvinocaridid shrimps live in hydrothermal vents, where is a wicked environment with highly toxic chemistry, hypoxia, acidic pH, and sulfide deposits. In order to adapt to this environment, change in energy metabolism may be one of the primary factors. However, the genetic basis of energy metabolism underlying this environment remains unexplored. Here, we present the first systematic investigation of mitochondrial genes in Alvinocarididae. The analysis demonstrated that ATP6, ND4 and ND6 were subjected to strong positive selection leading to last common ancestors of Alvinocarididae, and ATP8, ND5, COX1 and COX2 were determined to have undergone positive selection in the interior lineages of Alvinocarididae. Considering that about 95% of ATP is supplied by mitochondria via oxidative phosphorylation, and body detoxification process associated with cytochrome c. Positive selection in these genes suggested that Alvinocaridid shrimps might have acquired an enhanced capacity for energy metabolism and detoxification in extreme hydrothermal vent field.     

Combining otolith chemistry and telemetry to assess diadromous migration in pinkeye mullet, <Emphasis Type="Italic">Trachystoma petardi</Emphasis> (Actinopterygii,Mugiliformes)

Little is currently known regarding microbial community structure, and the environmental factors influencing it, within the anchialine ecosystem, defined as near-shore, land-locked water bodies with subsurface connections to the ocean and groundwater aquifer. The Hawaiian Archipelago is home to numerous anchialine habitats, with some on the islands of Maui and Hawaii harboring unique, laminated orange cyanobacterial–bacterial crusts that independently assembled in relatively young basalt fields. Here, benthic and water column bacterial and micro-eukaryotic communities from nine anchialine habitats on Oahu, Maui, and Hawaii were surveyed using high-throughput amplicon sequencing of the V6 (Bacteria-specific) and V9 (Eukarya-biased) hypervariable regions of the 16S- and 18S-rDNA genes, respectively. While benthic communities from habitats with cyanobacterial–bacterial crusts were more similar to each other than to ones lacking it on the same island, each habitat had distinct benthic and water column microbial communities. Analyses of the survey data in the context of environmental factors identified salinity, site, aquifer, and watershed as having the highest explanatory power for the observed variation in microbial diversity and community structure, with lesser drivers being annual rainfall, longitude, ammonium, and dissolved organic carbon. Our results epitomize the abiotic and biotic uniqueness characteristic of individual habitats comprising the Hawaiian anchialine ecosystem.     

Haplotype diversity of mt<Emphasis Type="Italic">COI</Emphasis> in the fall webworm <Emphasis Type="Italic">Hyphantria cunea</Emphasis> (Lepidoptera: Arctiidae) in introduced regions in China,Iran, Japan,Korea, and its homeland,the United States

Hyphantria cunea (Drury) has colonized many countries outside its native range of North America and has become a model species for studies of the colonization and subsequent adaptation of agricultural pests. Molecular genetic analyses can clarify the origin and subsequent adaptations to non-native habitats. Using the mitochondrial COI gene, we examined the genetic relationships between invasive populations (China, Iran, Japan, and Korea) and native populations (i.e., the United States). The Jilin (China) and Guilan (Iran) populations showed nine previously unknown haplotypes that differed from those found in the south–central United States, suggesting multiple colonization events and different regions of invasion. A dominant mtDNA haplotype in populations in the United States was shared by all of the populations investigated, suggesting that H. cunea with that haplotype have successfully colonized China, Iran, Japan, and Korea.     

Genetic exchange between anchialine cave populations by means of larval dispersal: the case of a new gastropod species Neritilia cavernicola

Despite being limited to caves, many anchialine taxa have disjunct insular distributions, which raises questions about their origins and colonization history. This study deals with the new gastropod Neritilia cavernicola sp. n. (Neritopsina: Neritiliidae) from anchialine caves on two islands in the Philippines that are separated by the deep Bohol Strait and situated 200 km apart along the coastline of Cebu Island. Neritilia cavernicola is an obligate stygobiont and most closely resembles Neritilia littoralis , which lives in interstitial waters of the Nansei-shoto Islands, Japan. Its eggs and larval shells are identical to those of other Neritilia species, despite their different adult habitats. This suggests a marine planktotrophic phase (as occurs in amphidromous riverine species of Neritilia ), and consequent migration between islands via ocean currents. Here we present the first genetic structure for anchialine cave organisms; comparisons of 1276 bp sequences from mitochondrial cytochrome oxidase I show no evidence of genetic isolation between the islands. All individuals evidently are part of a panmictic population and the low vagility of adults and their seemingly isolated cave habitats do not limit gene flow in N. cavernicola . This migration model, based on marine larval dispersal, may be widely applicable to anchialine stygobites with insular distributions, as many such organisms (including shrimps, crabs and fishes) are phylogenetically allied to amphidromous species.     

Genetic determinants of Tibetan high-altitude adaptation

Some highland populations have genetic adaptations that enable their successful existence in a hypoxic environment. Tibetans are protected against many of the harmful responses exhibited by non-adapted populations upon exposure to severe hypoxia, including elevated hemoglobin concentration (i.e., polycythemia). Recent studies have highlighted several genes subject to natural selection in native high-altitude Tibetans. Three of these genes, EPAS1, EGLN1 and PPARA, regulate or are regulated by hypoxia inducible factor, a principal controller of erythropoiesis and other organismal functions. Uncovering the molecular basis of hypoxic adaptation should have implications for understanding hematological and other adaptations involved in hypoxia tolerance. Because the hypoxia response involves a variety of cardiovascular, pulmonary and metabolic functions, this knowledge would improve our understanding of disease mechanisms and could ultimately be translated into targeted therapies for oxygen deprivation, cardiopulmonary and cerebral pathologies, and metabolic disorders such as diabetes and obesity.     

Metabolic profiling of hypoxic cells revealed a catabolic signature required for cell survival

Hypoxia is one of the features of poorly vascularised areas of solid tumours but cancer cells can survive in these areas despite the low oxygen tension. The adaptation to hypoxia requires both biochemical and genetic responses that culminate in a metabolic rearrangement to counter-balance the decrease in energy supply from mitochondrial respiration. The understanding of metabolic adaptations under hypoxia could reveal novel pathways that, if targeted, would lead to specific death of hypoxic regions. In this study, we developed biochemical and metabolomic analyses to assess the effects of hypoxia on cellular metabolism of HCT116 cancer cell line. We utilized an oxygen fluorescent probe in anaerobic cuvettes to study oxygen consumption rates under hypoxic conditions without the need to re-oxygenate the cells and demonstrated that hypoxic cells can maintain active, though diminished, oxidative phosphorylation even at 1% oxygen. These results were further supported by in situ microscopy analysis of mitochondrial NADH oxidation under hypoxia. We then used metabolomic methodologies, utilizing liquid chromatography-mass spectrometry (LC-MS), to determine the metabolic profile of hypoxic cells. This approach revealed the importance of synchronized and regulated catabolism as a mechanism of adaptation to bioenergetic stress. We then confirmed the presence of autophagy under hypoxic conditions and demonstrated that the inhibition of this catabolic process dramatically reduced the ATP levels in hypoxic cells and stimulated hypoxia-induced cell death. These results suggest that under hypoxia, autophagy is required to support ATP production, in addition to glycolysis, and that the inhibition of autophagy might be used to selectively target hypoxic regions of tumours, the most notoriously resistant areas of solid tumours.     

Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation

Pikas originated in Asia and are small lagomorphs native to cold climates. The plateau pika, Ochotona curzoniae is a keystone species on the Qinghai-Tibet Plateau and an ideal animal model for hypoxic adaptation studies. Altered mitochondrial function, especially cytochrome c oxidase activity, is an important factor in modulation of energy generation and expenditure during cold and hypoxia adaptation. In this study, we determined the complete nucleotide sequence of the O. curzoniae mitochondrial genome. The plateau pika mitochondrial DNA is 17,131bp long and encodes the complete set of 37 proteins typical for vertebrates. Phylogenetic analysis based on concatenated heavy-strand encoded protein-coding genes revealed that pikas are closer to rabbit and hare than to rat. This suggests that rabbit or hare would be a good control animal for pikas in cold and hypoxia adaptation studies. Fifteen novel mitochondrial DNA-encoded amino acid changes were identified in the pikas, including three in the subunits of cytochrome c oxidase. These amino acid substitutions potentially function in modulation of mitochondrial complexes and electron transport efficiency during cold and hypoxia adaptation.     

Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation

Chinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to the other members of the subfamily Colobinae (or leaf-eating monkeys), these endangered primates are unique in being adapted to a high altitude environment and display a remarkable ability to tolerate low temperatures and hypoxia. They thus offer an interesting organismal model of adaptation to extreme environmental stress. Mitochondria generate energy by oxidative phosphorylation (OXPHOS) and play important roles in oxygen usage and energy metabolism. We analyzed the mitochondrial genomes of two Chinese snub-nosed monkey species and eight other colobines in the first attempt to understand the genetic basis of high altitude adaptation in non-human primates. We found significant evidence of positive selection in one Chinese snub-nosed monkey, Rhinopithecus roxellana, which is suggestive of adaptive change related to high altitude and cold weather stress. In addition, our study identified two potentially important adaptive amino acid residues (533 and 3307) in the NADH2 and NADH6 genes, respectively. Surprisingly, no evidence for positive selection was found in Rhinopithecus bieti (the other Chinese snub-nosed monkey analyzed). This finding is intriguing, especially considering that R. bieti inhabits a higher altitudinal distribution than R. roxellana. We hypothesize that a different adaptive genetic basis to high altitude survival exists in R. bieti from those seen in other mammals, and that positive selection and functionally associated mutations in this species may be detected in nuclear genes related to energy and oxygen metabolism. More information on the structure, function, and evolution of mitochondrial and nuclear genomes in Chinese snub-nosed monkeys is required to reveal the molecular mechanisms that underlie adaptations to high altitude survival in non-human primates.     

Diurnal dynamics of the microbial loop in peatlands: structure, function and relationship to environmental parameters

Globally, introductions of alien species are increasingly common, with invasive predators potentially having detrimental effects via predation on native species. However, native prey may avoid predation by adopting new behaviors. To determine whether invasive fish populations consume endemic shrimp in invaded Hawaiian anchialine habitats or if adopted patterns of diel migration prevents predation as previously hypothesized, a total of 183 invasive poeciliids (158 Gambusia affinis and 25 Poecilia reticulata) were collected for gut content analyses from four anchialine sites during wet and dry seasons on the islands of Hawai‘i and Maui. Predation on shrimp was not detected in habitats where they retreat exclusively into the underlying aquifer diurnally and only emerge nocturnally. However, low levels of predation were detected (7/65 fishes, only by Gambusia affinis) at Waianapanapa Cave, Maui, where shrimp retreat into both the aquifer and a cave during the day. Thus, adopted behavioral responses to invasive fishes generally, though not universally, prevent predation on endemic Hawaiian anchialine shrimps. However, non-consumptive effects resulting from behavioral modification of shrimps may have appreciable impacts on the Hawaiian anchialine ecosystem and warrant further study.     

Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India

Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 for COI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes, respectively. Almost all species were represented by 2–3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis, Liodrosophila nitida, Lordiphosa parantillaria, Lordiphosa ayarpathaensis, Scaptomyza himalayana, Scaptomyza tistai, Zaprionus grandis and Stegana minuta are provided to public domains through this study.     

Host-use pattern of the shrimp <Emphasis Type="Italic">Periclimenes paivai</Emphasis> on the scyphozoan jellyfish <Emphasis Type="Italic">Lychnorhiza lucerna</Emphasis>: probing for territoriality and inferring its mating system

In symbiotic crustaceans, host-use patterns vary broadly. Some species inhabit host individuals solitarily, other species live in heterosexual pairs, and even other species live in aggregations. This disparity in host-use patterns coupled with considerable differences in host ecology provide opportunities to explore how environmental conditions affect animal behavior. In this study, we explored whether or not symbiotic crustaceans inhabiting relatively large and structurally complex host species live in aggregations. We expected Periclimenes paivai, a small caridean shrimp that lives among the tentacles of the large and morphologically complex scyphozoan jellyfish Lychnorhiza lucerna, to live in groups given that the host traits above constraint host-monopolization behaviors by symbiotic crustaceans. We described the population distribution of P. paivai during a bloom of L. lucerna near the mouth of the Paraíba River estuary in Paraíba, Brazil. The population distribution of P. paivai did not differ statistically from a random Poisson distribution. Male shrimps were most often found dwelling on the surface of L. lucerna individuals as small groups (2–4 individuals), in agreement with expectations. Periclimenes paivai is a sexually dimorphic species with males attaining smaller average body sizes than females and exhibiting no elaborated weaponry (claws). Females, but not males, experience positive allometry in cheliped size and were found living solitarily in small but not large host individuals. The above suggest that females might be territorial or that they might be competing for resources (i.e., food) likely expected to impact their reproductive output. Our results agree, but only partially, with the idea that large and morphologically complex host species should harbor non-territorial gregarious symbiotic crustaceans. Symbiotic crustaceans represent excellent models to improve our understanding about the conditions driving the social behavior of marine organisms.     

Symbiotic partner specificity and dependency of two gobies (<Emphasis Type="Italic">Apocryptodon punctatus</Emphasis> and <Emphasis Type="Italic">Acentrogobius</Emphasis> sp. A) and four alpheid shrimps inhabiting the temperate estuary of southern Japan

We collected two gobies, Apocryptodon punctatus and Acentrogobius sp. A, and four alpheid shrimps from an estuary in southern Japan, to identify the symbiotic shrimps with gobies and to understand their partner specificity and dependency. Analysis based on generalized linear models identified two specific partners for each goby. A. punctatus frequently coexisted with partners and showed similar habitats, suggesting that this goby might be an obligate mutualist. Acentrogobius sp. A had lower rates of coexistence and appeared in habitats different from one of its partners, suggesting that this goby might be a facultative mutualist.     

High-Resolution Respirometry in Diagnostics of Mitochondrial Diseases Caused by Mitochondrial Complex I Deficiency

Mitochondrial complex I deficiency (CID) is one of the most common defects in the OXPHOS system; it represents more than 30% cases of mitochondrial diseases. The group is characterized by clinical and genetic heterogeneity and comprises several nosological forms. The most prevalent phenotypes of CID are Leber hereditary optic neuropathy (LHON) and Leigh syndrome. In this study we have analyzed skin fibroblasts from 11 patients with mutations in mtDNA, which cause LHON or Leigh-like phenotypes (m.11778 G>A (n = 3), m.3460 A>G (n = 2), m.3635 G>A (n = 1), m.3308 T>G (n = 2), m.3472 T>C (n = 1)), and 2 patients with earlier unknown substitutions m.3945 C>A and m.14441 T>C. High-resolution respirometry (HRR) was performed for complex analysis of the mitochondrial respiratory function in intact and permeabilized fibroblasts of patients and healthy controls. Flux control ratios in intact cells R/E, (R-L)/E were raised compared to the control. Rates of R, E, L normalized on the citrate synthase (CS) activity were statistically different (p < 0.05) between patients and controls. In permeabilized fibroblasts we have found statistically significant differences (p < 0.05) in ratios СII/E, Rot/E, R/CII, CI/CII between groups. These data highlight dysfunctions of the OXPHOS system, particularly CI. Increased CS activity and decreased CI/CII ratio suggest a compensatory metabolic response to the respiratory chain dysfunction. Our results show applicability of HRR in revealing biochemical abnormalities of mitochondrial complex I in fibroblasts of patients with LHON and Leigh-like syndrome. We also suggest HRR to be a useful method for inspection of new mutations causing mitochondrial complex I deficiency.     

鲸类低氧耐受的分子机制初探:基于HIF1α和TSC1基因的生物信息学分析

鲸类(Cetacea)具有超强潜水能力,长时间潜水造成的体内低氧是其适应完全水生生活面临的挑战之一.为了克服体内低氧环境,鲸类产生了一系列低氧耐受相关的解剖和生理等方面的适应特征,然而这一适应的分子机制仍不清楚.本研究选择在细胞感知和适应内环境氧分压变化的过程中发挥重要作用的低氧诱导因子(Hy-poxia-induci...     

Geographic variation in thermal tolerance and strategies of heat shock protein expression in the land snail <Emphasis Type="Italic">Theba pisana</Emphasis> in relation to genetic structure

Land snails are exposed to conditions of high ambient temperature and low humidity, and their survival depends on a suite of morphological, behavioral, physiological, and molecular adaptations to the specific microhabitat. We tested in six populations of the land snail Theba pisana whether adaptations to different habitats affect their ability to cope with thermal stress and their strategies of heat shock protein (HSP) expression. Levels of Hsp70 and Hsp90 in the foot tissue were measured in field-collected snails and after acclimation to laboratory conditions. Snails were also exposed to various temperatures (32 up to 54 °C) for 2 h and HSP messenger RNA (mRNA) levels were measured in the foot tissue and survival was determined. To test whether the physiological and molecular data are related to genetic parameters, we analyzed T. pisana populations using partial sequences of nuclear and mitochondrial DNA ribosomal RNA genes. We show that populations collected from warmer habitats were more thermotolerant and had higher constitutive levels of Hsp70 isoforms in the foot tissue. Quantitative real-time polymerase chain reaction (PCR) analysis indicated that hsp70 and hsp90 mRNA levels increased significantly in response to thermal stress, although the increase in hsp70 mRNA was larger compared to hsp90 and its induction continued up to higher temperatures. Generally, warm-adapted populations had higher temperatures of maximal induction of hsp70 mRNA synthesis and higher upper thermal limits to HSP mRNA synthesis. Our study suggests that Hsp70 in the foot tissue of T. pisana snails may have important roles in determining stress resistance, while Hsp90 is more likely implicated in signal transduction processes that are activated by stress. In the phylogenetic analysis, T. pisana haplotypes were principally divided into two major clades largely corresponding to the physiological ability to withstand stress, thus pointing to genetically fixed tolerance.     

Adaptations of fish species to oxygen depletion in a central Amazonian floodplain lake

Pronounced seasonal and daily oxygen concentration changes are characteristic for Amazonian floodplain lakes. Studies on the fish fauna of the Lago Camaleão, Solimões River, Amazonas, Brazil, showed several fish species which are able to survive prolonged periods of heavy hypoxia. Twenty species belonging to eight families were observed in the laboratory in order to determine their respiratory adaptations to hypoxic conditions and oxygen concentrations at which the fish present respiratory adaptations. Finally, the fish species were distributed throughout the habitats of Lake Camaleão according to their adaptation responses. Ten fish species used the surface water for aquatic surface respiration, four species used atmospheric oxygen for aerial respiration, four species used oxygen supplied by the exudation of the roots of floating macrophytes and two exhibited a high tolerance to hypoxic conditions, and well-developed physiological biochemical mechanisms. The fish fauna is well adapted to low oxygen concentrations. The large variety of morpho-anatomical adaptations associated with biochemical and physiological mechanisms to tolerate hypoxic and anoxic conditions enable the 20 fish species to exploit several habitats of Lago Camaleão, such as floating aquatic macrophyte meadows, open water and near the shoreline.     

Genomic Signatures of Selection between Urban and Rural Populations of Black Garden Ant <Emphasis Type="Italic">Lasius niger</Emphasis>

Black garden ant L. niger is known as a dominant species of urban ant fauna in Europe. Successful propagation of L. niger in transformed ecosystems was associated with behavioral traits in many surveys; however, molecular and genetic basis of such adaptation was never studied. In the present study, genomes of populations from the city of Moscow and natural habitats of Moscow oblast are compared. Pooled samples from rural and urban habitats are collected and sequenced with Illumina HiSeq. SNP frequency, Tajima’s D, and fixation index are estimated with PoPoolation and Popoolation2 software. SNP frequencies are significantly different in 64 genes according to Fisher’s exact test. Some of these genes are detected as affected by recent selection. Out of 64 genes, 26 encode retrotransposon proteins. The genes of immune response to viral and fungal infections, fatty acid synthases, and elements of the Hippo/Fat pathway have different SNP frequencies between populations. Certain retrotransposon genes also can be under selection. It is important to note that repressors and mediators of RNA polymerase II are significantly different between urban and rural populations of L. niger. These genes can influence retrotransposon mobility.