The complete mitochondrial transcript of the red tail loach Yasuhikotakia modesta as assembled from RNAseq (Teleostei: Botiidae)

Here, we present the first complete mitochondrial genome of the Red Tailed Loach Yasuhikotakia modesta (Teleostei: Botiidae) from Thailand, assembled from next-generation transcriptome sequencing data. The assembled transcript corresponds to the full length mitochondrial genome of Y. modesta, which measured 16,865 bp in length, and contained 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. A slight A+T bias was observed in the mitogenome of Y. modesta with an overall base composition of 32.2% A, 25.8% T, 26.4% C, and 15.4% G, and a GC content of 41.8%. The gene arrangement was identical to that of previously described loach mitogenomes

Localization of copper and copper transporters in the human brain

Disturbances in brain copper result in rare and severe neurological disorders and may play a role in the pathogenesis and progression of multiple neurodegenerative diseases. Our current understanding of mammalian brain copper transport is based on model systems outside the central nervous system and no data are available regarding copper transport systems in the human brain. To address this deficit, we quantified regional copper concentrations and examined the distribution and cellular localization of the copper transport proteins Copper transporter 1, Atox1, ATP7A, and ATP7B in multiple regions of the human brain using inductively coupled plasma-mass spectrometry, Western blot and immunohistochemistry. We identified significant relationships between copper transporter levels and brain copper concentrations, supporting a role for these proteins in copper transport in the human brain. Interestingly, the substantia nigra contained twice as much copper than that in other brain regions, suggesting an important role for copper in this brain region. Furthermore, ATP7A levels were significantly greater in the cerebellum, compared with other brain regions, supporting an important role for ATP7A in cerebellar neuronal health. This study provides novel data regarding copper regulation in the human brain, critical to understand the mechanisms by which brain copper levels can be altered, leading to neurological disease

More non-native fish species than natives, and an invasion of Malawi cichlids, in ancient Lake Poso, Sulawesi, Indonesia

Ancient Lake Poso in Central Sulawesi, Indonesia, is among the deepest lakes in Asia, and hosts a largely endemic fauna of fishes, crustaceans, and molluscs. Introduction of non-native fish species started at least a century ago to foster local fish production. Recent fieldwork suggests that introduction of non-native fishes is ongoing, including species that originate from the ornamental pet trade. These include the hybridogenic ornamental “flowerhorn” cichlid, a fish that spread rapidly in Sulawesi’s Malili Lakes, and the “golden cichlid,” Melanochromis auratus from African Lake Malawi. This popular aquarium species colonized Lake Poso even more rapidly than the flowerhorn, and is omnipresent at benthic habitats across most of the lake. Here, we list records of 17 non-native fish species from Lake Poso, present the first assessment of golden cichlid stomach contents outside of their native habitat, report the occurrences of non-native crustaceans, molluscs and plants, and discuss potential impacts on the native fauna and ecosystem. Most of the non-native species have established substantial populations, and it appears very plausible that the non-native fauna affects endemics. This is supported by the finding that golden cichlid stomachs contained a broad spectrum of items, including fish, their scales, fins, eggs and larvae, and various invertebrates. We conclude that non-native species introduction poses a substantial and increasing threat to the Lake Poso fauna, a major hotspot of aquatic biodiversity in the Wallacea region

Inflammation and convergent placenta gene co-option contributed to a novel reproductive tissue

Highlights: • Pelvic brooding induces tissue-specific changes in gene expression • Inflammatory signaling characterizes transcriptome of the egg-anchoring plug • Similar to embryo implantation, the plug likely evolved from an inflammatory response • Mammalian placenta genes were independently co-opted into the plug Summary: The evolution of pregnancy exposes parental tissues to new, potentially stressful conditions, which can trigger inflammation.1 Inflammation is costly2,3 and can induce embryo rejection, which constrains the evolution of pregnancy.1 In contrast, inflammation can also promote morphological innovation at the maternal-embryonic interface as exemplified by co-option of pro-inflammatory signaling for eutherian embryo implantation.1,4,5 Given its dual function, inflammation could be a key process explaining how innovations such as pregnancy and placentation evolved many times convergently. Pelvic brooding ricefishes evolved a novel “plug” tissue,6,7 which forms inside the female gonoduct after spawning, anchors egg-attaching filaments, and enables pelvic brooders to carry eggs externally until hatching.6,8 Compared to pregnancy, i.e., internal bearing of embryos, external bearing should alleviate constraints on inflammation in the reproductive tract. We thus hypothesized that an ancestral inflammation triggered by the retention of attaching filaments gave rise to pathways orchestrating plug formation. In line with our hypothesis, histological sections of the developing plug revealed signs of gonoduct injuries by egg-attaching filaments in the pelvic brooding ricefish Oryzias eversi. Tissue-specific transcriptomes showed that inflammatory signaling dominates the plug transcriptome and inflammation-induced genes controlling vital processes for plug development such as tissue growth and angiogenesis were overexpressed in the plug. Finally, mammalian placenta genes were enriched in the plug transcriptome, indicating convergent gene co-option for building, attaching, and sustaining a transient tissue in the female reproductive tract. This study highlights the role of gene co-option and suggests that recruiting inflammatory signaling into physiological processes provides a fast-track to evolutionary innovation

MRI Assessment of Swallow Muscle Activation with the Swallow Exercise Aid and with Conventional Exercises in Healthy Volunteers: An Explorative Biomechanical Study

Swallowing muscle strength exercises are effective in restoring swallowing function. In order to perform the exercises with progressive load, the swallow exercise aid (SEA) was developed. Precise knowledge on which muscles are activated with swallowing exercises, especially with the SEA, is lacking. This knowledge would aid in optimizing the training program to target the relevant swallowing muscles, if necessary. Three healthy volunteers performed the three SEA exercises (chin tuck against resistance, jaw opening against resistance and effortful swallow) and three conventional exercises [conventional effortful swallow (cES), Shaker and Masako] in supine position inside an MRI scanner. Fast muscle functional MRI scans (generating quantitative T2-maps) were made immediately before and after the exercises. Median T2 values at rest and after exercise were compared to identify activated muscles. After the three SEA exercises, the suprahyoid, infrahyoid, sternocleidomastoid, and lateral pterygoid muscles showed significant T2 value increase. After the Shaker, the lateral pterygoid muscles did not show such an increase, but the three other muscle groups did. The cES and Masako caused no significant increase in any of these muscle groups. During conventional (Shaker) exercises, the suprahyoid, infrahyoid, and sternocleidomastoid muscles are activated. During the SEA exercises, the suprahyoid, infrahyoid, sternocleidomastoid, and lateral pterygoid muscles are activated. The findings of this explorative study further support the potential of the SEA to improve swallowing rehabilitation

MRI Assessment of Swallow Muscle Activation with the Swallow Exercise Aid and with Conventional Exercises in Healthy Volunteers: An Explorative Biomechanical Study

Swallowing muscle strength exercises are effective in restoring swallowing function. In order to perform the exercises with progressive load, the swallow exercise aid (SEA) was developed. Precise knowledge on which muscles are activated with swallowing exercises, especially with the SEA, is lacking. This knowledge would aid in optimizing the training program to target the relevant swallowing muscles, if necessary. Three healthy volunteers performed the three SEA exercises (chin tuck against resistance, jaw opening against resistance and effortful swallow) and three conventional exercises [conventional effortful swallow (cES), Shaker and Masako] in supine position inside an MRI scanner. Fast muscle functional MRI scans (generating quantitative T2-maps) were made immediately before and after the exercises. Median T2 values at rest and after exercise were compared to identify activated muscles. After the three SEA exercises, the suprahyoid, infrahyoid, sternocleidomastoid, and lateral pterygoid muscles showed significant T2 value increase. After the Shaker, the lateral pterygoid muscles did not show such an increase, but the three other muscle groups did. The cES and Masako caused no significant increase in any of these muscle groups. During conventional (Shaker) exercises, the suprahyoid, infrahyoid, and sternocleidomastoid muscles are activated. During the SEA exercises, the suprahyoid, infrahyoid, sternocleidomastoid, and lateral pterygoid muscles are activated. The findings of this explorative study further support the potential of the SEA to improve swallowing rehabilitation

Vitamin K1 to slow vascular calcification in haemodialysis patients (VitaVasK trial): a rationale and study protocol.

VitaVasK is a prospective, randomized, parallel group, multicentre trial (EudraCT No.: 2010-021264-14) that will include 348 HD patients in an open-label, two-arm design. After baseline multi-slice computed tomography (MSCT) of the heart and thoracic aorta, patients with a coronary calcification volume score of at least 100 will be randomized to continue on standard care or to receive additional supplementation with 5 mg vitamin K1 orally thrice weekly. Treatment duration will be 18 months, and MSCT scans will be repeated after 12 and 18 months. Primary end points are the progression of thoracic aortic and coronary artery calcification (calculated as absolute changes in the volume scores at the 18-month MSCT versus the baseline MSCT). Secondary end points comprise changes in Agatston score, mitral and aortic valve calcification as well as major adverse cardiovascular events (MACE) and all-cause mortality. VitaVask also aims to record MACE and all-cause mortality in the follow-up period at 3 and 5 years after treatment initiation. This trial may lead to the identification of an inexpensive and safe treatment or prophylaxis of VC in HD patients

Integrating gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era