Evolutionary ecology of opsin gene sequence,expression and repertoire

Linking molecular evolution to biological function is a long‐standing challenge in evolutionary biology. Some of the best examples of this involve opsins, the genes that encode the molecular basis of light reception. In this issue of Molecular Ecology, three studies examine opsin gene sequence, expression and repertoire to determine how natural selection has shaped the visual system. First, Escobar‐Camacho et al. ( 2017 ) use opsin repertoire and expression in three Amazonian cichlid species to show that a shift in sensitivity towards longer wavelengths is coincident with the long‐wavelength‐dominated Amazon basin. Second, Stieb et al. ( 2017 ) explore opsin sequence and expression in reef‐dwelling damselfish and find that UV‐ and long‐wavelength vision are both important, but likely for different ecological functions. Lastly, Suvorov et al. ( 2017 ) study an expansive opsin repertoire in the insect order Odonata and find evidence that copy number expansion is consistent with the permanent heterozygote model of gene duplication. Together these studies emphasize the utility of opsin genes for studying both the local adaptation of sensory systems and, more generally, gene family evolution.     

狭义小奥德蘑属（膨瑚菌科,蘑菇目）的一个新系统

本文对狭义小奥德蘑属Oudemansiella s. str.的概念做了修订,在修订后的属中,狭义干蘑属Xerula s. str.的物种不纳入其中。在狭义小奥德蘑属下,提出了一个包含4个组O. sect. Oudemansiella、Mucidula、Dactylosporina 和 Radicatae的新系统。小奥德蘑组sect. Oudemansiella包括热带至南温带的一些物种,如新热带小奥德蘑O. platensis、澳洲小奥德蘑O. australis、旧热带小奥德蘑O. canarii和宽褶小奥德蘑O. crassifolia,这些物种的菌盖表皮为粘栅栏型,由菌丝组成,但其中常夹杂有链状排列的膨大细胞。粘蘑组sect. Mucidula包含北半球温带至亚热带的一些物种,如粘小奥德蘑O. mucida、网褶小奥德蘑O. venosolamellata和近粘小奥德蘑O. submucida,其菌盖表皮为粘子实层-栅栏型,由近棒状的顶端膨大细胞组成。小奥德蘑组和粘蘑组的物种,在外形和小生境上有相似之处,其担子果皆生于地表外的腐木上,菌柄上有或无菌环。刺孢组sect. Dactylosporina包含中南美洲那些孢子表面有指状凸起的物种。长根组sect. Radicatae由长根小奥德蘑O. radicata及其近缘种为代表,是该属中最大的组,包括该属其他三组之外的所有种。北美的O. americana、欧洲的O. caussei 和东亚的O. hongoi曾被置于小奥德蘑属中的白毛组O. sect. Albotomentosae或干蘑属的亮毛组X. sect. Hyalosetae,在本系统中它们没有纳入小奥德蘑属,因为它们可能代表一个单独的属。本文还提出了1新等级、32个新组合和1个新名称。     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Isolation, structure and properties of the C-terminal flanking peptide of preprocholecystokinin from rat brain

The C-terminal flanking peptide of preprocholecystokinin has been isolated from rat brain. Micro-sequence analysis revealed the primary structure: Ser-Ala-Glu-Asp-Tyr-Glu-Tyr-Pro-Ser. Arylsulphatase and mild acid hydrolysis suggested that both tyrosine residues are sulphated. The peptide was not active in bioassay systems that respond to CCK8; the significance of the conserved tripeptide Ser-Ala-Glu is discussed.     

Ovine coccidiosis: pathology of Eimeria ovinoidalis infection

Doses of sporulated oocysts of Eimeria ovinoidalis ranging from 10² to 5 × 10⁶ were given to 25 housed lambs aged between 5 and 13 weeks, most of which had been reared coccidia-free. Some had received an “immunizing” dose 3–4 weeks earlier. Lambs were killed between 8 and 21 days after inoculation (DAI) and the tissues were examined histologically. Doses higher than 10⁶ caused extensive loss of epithelial cells in the lower jejunum both from the surface and from the crypts at 10 DAI when first-generation meronts were mature. Doses of 10³ oocysts or more caused diarrhoea from about 13 DAI in both first and second infections; this was associated with massive invasion of the caecal epithelium by second-generation meronts and gamonts. Destruction of crypt stem cells by these stages led to denudation of the caecal mucosa, resulting in haemorrhagic enteritis, dehydration and delayed healing or death.     

Electrophysiological and immunocytochemical characterization of DRG neurons on an organosilane surface in serum-free medium

We are attempting to recreate a stretch reflex circuit on a patterned Bio-MEMS (bio-microelectromechanical systems) chip with deflecting micro-cantilevers. The first steps to recreate this system is to be able to grow individual components of the circuit (sensory neuron, motoneuron, skeletal muscle, and muscle spindle) on a patternable, synthetic substrate coating the MEMS device. Sensory neurons represent the afferent portion of the stretch reflex arc and also play a significant role in transmitting the signal from the muscle spindle to the spinal cord motoneurons. We have utilized a synthetic silane substrate N-1[3-(trimethoxysilyl) propyl) diethylenetriamine (DETA) on which to grow and pattern the cells. DETA forms a self-assembled monolayer on a variety of silicon substrates, including glass, and can be patterned using photolithography. In this paper, we have evaluated the growth of sensory neurons on this synthetic silane substrate. We have investigated the immunocytochemical and electrophysiological properties of the sensory neurons on DETA and compared the resultant properties with a biological control substrate (ornithine/laminin). Immunocytochemical studies revealed the survival and growth of all three subtypes of sensory neurons: trkA, trkB, and trkC on both surfaces. Furthermore, whole-cell patch clamp recordings were used to study the electrophysiological properties of the sensory neurons on the two surfaces. There were no significant differences in the electrical properties of the neurons grown on either surface. This is the first study analyzing the immunocytochemical and electrophysiological properties of sensory neurons grown long-term in a completely defined environment and on a nonbiological substrate.     

Arabidopsis XXT5 gene encodes a putative alpha-1,6-xylosyltransferase that is involved in xyloglucan biosynthesis

The function of a putative xyloglucan xylosyltransferase from Arabidopsis thaliana (At1g74380; XXT5) was studied. The XXT5 gene is expressed in all plant tissues, with higher levels of expression in roots, stems and cauline leaves. A T-DNA insertion in the XXT5 gene generates a readily visible root hair phenotype (root hairs are shorter and form bubble-like extrusions at the tip), and also causes the alteration of the main root cellular morphology. Biochemical characterization of cell wall polysaccharides isolated from xxt5 mutant seedlings demonstrated decreased xyloglucan quantity and reduced glucan backbone substitution with xylosyl residues. Immunohistochemical analyses of xxt5 plants revealed a selective decrease in some xyloglucan epitopes, whereas the distribution patterns of epitopes characteristic for other cell wall polysaccharides remained undisturbed. Transformation of xxt5 plants with a 35S::HA-XXT5 construct resulted in complementation of the morphological, biochemical and immunological phenotypes, restoring xyloglucan content and composition to wild-type levels. These data provide evidence that XXT5 is a xyloglucan alpha-1,6-xylosyltransferase, and functions in the biosynthesis of xyloglucan.     

The nucleotide exchange factor Ric-8A is a chaperone for the conformationally dynamic nucleotide-free state of Gαi1

Heterotrimeric G protein α subunits are activated upon exchange of GDP for GTP at the nucleotide binding site of Gα, catalyzed by guanine nucleotide exchange factors (GEFs). In addition to transmembrane G protein-coupled receptors (GPCRs), which act on G protein heterotrimers, members of the family cytosolic proteins typified by mammalian Ric-8A are GEFs for Gi/q/12/13-class Gα subunits. Ric-8A binds to Gα?GDP, resulting in the release of GDP. The Ric-8A complex with nucleotide-free Gαi1 is stable, but dissociates upon binding of GTP to Gαi1. To gain insight into the mechanism of Ric-8A-catalyzed GDP release from Gαi1, experiments were conducted to characterize the physical state of nucleotide-free Gαi1 (hereafter referred to as Gαi1[ ]) in solution, both as a monomeric species, and in the complex with Ric-8A. We found that Ric-8A-bound, nucleotide-free Gαi1 is more accessible to trypsinolysis than Gαi1?GDP, but less so than Gαi1[ ] alone. The TROSY-HSQC spectrum of [(15)N]Gαi1[ ] bound to Ric-8A shows considerable loss of peak intensity relative to that of [(15)N]Gαi1?GDP. Hydrogen-deuterium exchange in Gαi1[ ] bound to Ric-8A is 1.5-fold more extensive than in Gαi1?GDP. Differential scanning calorimetry shows that both Ric-8A and Gαi1?GDP undergo cooperative, irreversible unfolding transitions at 47° and 52°, respectively, while nucleotide-free Gαi1 shows a broad, weak transition near 35°. The unfolding transition for Ric-8A:Gαi1[ ] is complex, with a broad transition that peaks at 50°, suggesting that both Ric-8A and Gαi1[ ] are stabilized within the complex, relative to their respective free states. The C-terminus of Gαi1 is shown to be a critical binding element for Ric-8A, as is also the case for GPCRs, suggesting that the two types of GEF might promote nucleotide exchange by similar mechanisms, by acting as chaperones for the unstable and dynamic nucleotide-free state of Gα.     

Rank-Related Fitness Differences and Their Demographic Pathways in Semi-Free-Ranging Rhesus Macaques (<Emphasis Type=Italic>Macaca mulatta</Emphasis>)

Researchers have explored the fitness consequences of female dominance hierarchies in many primate populations, with most studies highlighting differences in age of maturation, fertility, and offspring survival. We use resampling techniques and van Tienderen’s (2000) elasticity path analysis to identify rank-related differences in finite rate of increase (λ) and their demographic correlates among segments of a semi-free-ranging rhesus macaque population. Higher-ranking population segments grew at greater rates for some portions of the 40-yr study period. The female members of these segments achieved these lifetime fitness differences through higher fertility and especially higher adult survival rates. This is the first clear evidence that social rank influences female primate adult survival, and is a crucial fitness component for any long-lived, slow-reproducing animal. Traditional methods of comparing lifespans, and other life history variables, among rank categories fail to identify most of the rank-related differences primarily because they require completed life histories that are available only on a small number of the females known in the population.