Two hundred years of zooplankton vertical migration research

Vertical migration is a geographically and taxonomically widespread behaviour among zooplankton that spans across diel and seasonal timescales. The shorter-term diel vertical migration (DVM) has a periodicity of up to 1 day and was first described by the French naturalist Georges Cuvier in 1817. In 1888, the German marine biologist Carl Chun described the longer-term seasonal vertical migration (SVM), which has a periodicity of ca. 1 year. The proximate control and adaptive significance of DVM have been extensively studied and are well understood. DVM is generally a behaviour controlled by ambient irradiance, which allows herbivorous zooplankton to feed in food-rich shallower waters during the night when light-dependent (visual) predation risk is minimal and take refuge in deeper, darker waters during daytime. However, DVMs of herbivorous zooplankton are followed by their predators, producing complex predator–prey patterns that may be traced across multiple trophic levels. In contrast to DVM, SVM research is relatively young and its causes and consequences are less well understood. During periods of seasonal environmental deterioration, SVM allows zooplankton to evacuate shallower waters seasonally and take refuge in deeper waters often in a state of dormancy. Both DVM and SVM play a significant role in the vertical transport of organic carbon to deeper waters (biological carbon sequestration), and hence in the buffering of global climate change. Although many animal migrations are expected to change under future climate scenarios, little is known about the potential implications of global climate change on zooplankton vertical migrations and its impact on the biological carbon sequestration process. Further, the combined influence of DVM and SVM in determining zooplankton fitness and maintenance of their horizontal (geographic) distributions is not well understood. The contrasting spatial (deep versus shallow) and temporal (diel versus seasonal) scales over which these two migrations occur lead to challenges in studying them at higher spatial, temporal and biological resolution and coverage. Extending the largely population-based vertical migration knowledge base to individual-based studies will be an important way forward. While tracking individual zooplankton in their natural habitats remains a major challenge, conducting trophic-scale, high-resolution, year-round studies that utilise emerging field sampling and observation techniques, molecular genetic tools and computational hardware and software will be the best solution to improve our understanding of zooplankton vertical migrations.     

The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays

Pathogenic variants in BRCA1 are associated with a greatly increased risk of hereditary breast and ovarian cancer (HBOC). With the increased availability and affordability of genetic testing, many individuals have been identified with BRCA1 variants of uncertain significance (VUSs), which are individually detected in the population too infrequently to ascertain a clinical risk. Functional assays can be used to experimentally assess the effects of these variants. In this study, we used multiplexed DNA repair assays of variants in the BRCA1 carboxyl terminus to functionally characterize 2,271 variants for homology-directed repair function (HDR) and 1,427 variants for cisplatin resistance (CR). We found a high level of consistent results (Pearson’s r = 0.74) in the two multiplexed functional assays with non-functional variants located within regions of the BRCA1 protein necessary for its tumor suppression activity. In addition, functional categorizations of variants tested in the multiplex HDR and CR assays correlated with known clinical significance and with other functional assays for BRCA1 (Pearson’s r = 0.53 to 0.71). The results of the multiplex HDR and CR assays are useful resources for characterizing large numbers of BRCA1 VUSs.     

Seed coat morphology and its systematic significance in Juncus L. (Juncaceae) in Egypt

The seed morphology of nine taxa of Juncus from Egypt has been investigated using light and scanning electron microscopy, to determine the importance of seed coat features as taxonomic characters. Macro- and micromorphological characters, including seed shape, color, size, seed appendages, epidermal cell shape, anticlinal boundaries, and outer periclinal cell wall and secondary cell wall sculpture are presented. Four types of seed appendages are recognized: (i) seeds with two appendages; (ii) seeds without appendages; (iii) seeds with minutely a piculate at one end; and (iv) seeds with minutely a piculate at both ends. Two types of anticlinal cell wall boundaries,(i) raised-channeled, straight and (ii) raised, straight or sinuous, and three different shapes of outer periclinal cell wall are described: (i) flat; (ii) concave; and (iii) flat to slightly concave. The secondary sculpture of the cell wall varies from striate to microreticulate or reticulate, and smooth to finely folded. Seed characters provide useful data for formulating the taxonomy of Juncus both on the subgeneric and sectional level. A key for the identification of the investigated taxa based on seed characters is provided.     

The tail tells the tale: taxonomy and biogeography of some Atlantic Chelidonura (Gastropoda: Cephalaspidea: Aglajidae) inferred from nuclear and mitochondrial gene data

Several western Atlantic species of Chelidonura have been described mainly based on differences in colour pattern. Sequence data from two mitochondrial [cytochrome oxidase I (COI), 16S] genes and a nuclear [histone 3 (H3)] gene have revealed that all colour forms previously recognized from across the Caribbean, Bahamas, and Bermuda belong to the same species, Chelidonura berolina. However, several specimens from the Bahamas are genetically and morphologically distinct and are herein described as a new species, Chelidonura normani sp. nov. Externally, C. normani can only be distinguished from C. berolina by the morphology of the posterior end of the body and not by colour pattern. Both C. berolina and C. normani are genetically and morphologically distinct from the eastern Atlantic species Chelidonura africana, but the split between C. berolina and C. normani predates the split between C. berolina and C. africana. All three species differ in their protoconch morphology, which suggests different developmental modes. Furthermore, all three species display a broad variation in colour pattern, which raises questions on the biological significance of colour in this group. The reasons for the divergence between C. berolina and C. normani remain unknown but could be related to the complex geological history of the western Atlantic. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1077–1095.     

Tests of Significance for Combined Measures of Plant Stability and Performance

Of significance in plant breeding is to develop varieties that are stable and have optimum performance, such as high yield, in different target environments. As such, selection should be on a measure that combines stability and performance. In this study, we examine the distributions for three nonparametric and three parametric measures for combined stability and performance and show that the F statistic from an analysis of variance may be used to test for differences among genotypes with regard to these measures. Recommendations are made based on the size and power of the F statistic for each of the measures. Application of the theoretical results is demonstrated using data on 14 varieties of oats in 18 locations.     

Crystal structure of thioredoxin 1 from Cryptococcus neoformans at 1.8 Å resolution shows unexpected plasticity of the loop preceding the catalytic site

An elevated prevalence of cryptococcal infection is a tendency in low-income countries and constitutes a global public health problem due to factors such as the limited efficacy of antifungal therapy and the AIDS/transplant immunocompromised patients. The fungus Cryptococcus neoformans, implicated in this burden, has had several genes validated as drug targets. Among them, the thioredoxin system is one of the major regulators of redox homeostasis and antioxidant defense acting on protein disulfide bonds. Thioredoxin 1 from C. neoformans (CnTrx1) was cloned and expressed in E. coli and the recombinant protein was purified and crystallized. Functional assay shows that CnTrx1 catalyzes the reduction of insulin disulfide bonds using dithiothreitol, while acting as a monomer in solution. The crystal structure of oxidized CnTrx1 at 1.80 Å resolution presents a dimer in the asymmetric unit with typical Trx-fold. Differences between the monomers in the asymmetric unit are found specially in the loop leading to the Cys-Gly-Pro-Cys active-site motif, being even larger when compared to those found between reduced and oxidized states of other thioredoxins. Although the thioredoxins have been isolated and characterized from many organisms, this new structural report provides important clues for understanding the binding and specificity of CnTrx1 to its targets.     

Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila

Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.     

Chemical constituents from the stems of Tripterygium regelii

Phytochemical investigation on the stems of Tripterygium regelii resulted in the isolation of fourteen compounds, including six flavonoids (1–6), seven lignans (7–13), and one cyanogenic glycoside (14). This is the first report of the four dimeric flavonoids bis-8, 8′-catechinylmethane (2), bis (8-epicatechinyl) methane (3), bis-6, 8′-catechinylmethane (4) and montahomobisflavan B (5) from a species of Tripterygium. Previously, these dimeric flavonoids have been mainly identified from species of gymnosperms. This research has shown that the main secondary metabolisms identified in T. regelii were flavonoids and lignans. These data enable this species to be differentiated from T. wilfordii and T. hypoglaucum that contain the triptolide-resembling diterpenoids.     

Cyclopeptide alkaloids

In this review, we discuss cyclopeptide alkaloids, their plant origin, and the way of separation, spectral analysis done for structure elucidation, stereochemistry, and their biological activities. In addition, we discuss briefly the chemosystematic significance of the cyclopeptide alkaloids based on their discovery in the family Olacaceae. Dedicated with regards to Profs. J. Bruhn, E.E.A. El-Khrisy, S. Yamamura and K.B.G. Torssell on their 60th, 65th, 70th and 80th birthdays, respectively.     

Analysis of connection networks among miRNAs differentially expressed in early gastric cancer for disclosing some biological features of disease development

This paper first identified differentially expressed miRNAs associated with early gastric cancer and then respectively constructed relevant connection networks among the identified differentially expressed miRNAs that corresponded to early gastric cancer and control tissues. Twenty-three differentially expressed miRNAs were identified, 18 of which were different with the related results on the same data, and they provide great discriminatory power between patients and controls. There are not only conserved unchangeable sub-networks but also different sub-networks between the two connection networks. From the consistency and differences between two connection networks, we disclosed several new biological features that promote early gastric cancer development. This study shows 23 miRNAs that are early gastric cancer-specific and are worthy to do further experimental studies. The revealed biological features for early gastric cancer will provide new insights into improved understanding of the molecular mechanisms of this disease.