The diversity and ecological significance of Protozoa

The unicellular eukaryotes are currently grouped in the kingdom Protista, together with their multicellular relatives. The inclusion of protozoa, algae and water moulds in a single taxon has resulted in nomenclatural problems, academic homelessness, and a reduction in their teaching. There are around 40 000 described protozoan protist species. Protozoa are principally grazers of bacteria, increasing mineralization and making nutrients more available to other organisms; most are aquatic, but they are also widespread animal parasites and symbionts. Their biomass, role in food chains, roles as mutualists and pathogens, and value as biomonitors are reviewed. To assess the role of protozoa in ecosystems more accurately, the current poor taxonomic standards in ecological work on protozoa must be improved. The manpower to respond to existing and new challenges in the field is declining as protozoology disappears from university courses and this problem needs to be addressed.     

The functional diversity of protein lysine methylation

Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.     

The magnitude and significance of Ca2+ domains for release of neurotransmitter

It is now widely accepted that localized high concentrations of Ca²⁺ (Ca²⁺ domains) play a major role in controlling the time course of neurotransmitter release. In the present work we calculate the magnitude and the time course of Ca²⁺ domains that evolve in the vicinity of a Ca²⁺ channel and an adjacent release site. In the calculations we consider a accurately dimensioned Ca²⁺ channel. Moreover, the Ca²⁺ current is continuously adjusted with regard to the accumulated intracellular Ca²⁺ and, in addition, endogenous buffers are considered. The calculations, carried out by the software FIDAP, based on finite element method, show that the Ca²⁺ concentrations achieved near the release sites are significantly lower than claimed by other investigators. Furthermore, we present arguments indicating that the Ca²⁺ domains, regardless of their magnitude, do not play a role in controlling the time course of release of neurotransmitter. Also belongs to the Center for Neural Computation. Parnas is the Greenfield Professor of Neurobiology.     

Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance

Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.     

The functional role of producer diversity in ecosystems

Over the past several decades, a rapidly expanding field of research known as biodiversity and ecosystem functioning has begun to quantify how the world's biological diversity can, as an independent variable, control ecological processes that are both essential for, and fundamental to, the functioning of ecosystems. Research in this area has often been justified on grounds that (1) loss of biological diversity ranks among the most pronounced changes to the global environment and that (2) reductions in diversity, and corresponding changes in species composition, could alter important services that ecosystems provide to humanity (e.g., food production, pest/disease control, water purification). Here we review over two decades of experiments that have examined how species richness of primary producers influences the suite of ecological processes that are controlled by plants and algae in terrestrial, marine, and freshwater ecosystems. Using formal meta-analyses, we assess the balance of evidence for eight fundamental questions and corresponding hypotheses about the functional role of producer diversity in ecosystems. These include questions about how primary producer diversity influences the efficiency of resource use and biomass production in ecosystems, how primary producer diversity influences the transfer and recycling of biomass to other trophic groups in a food web, and the number of species and spatial /temporal scales at which diversity effects are most apparent. After summarizing the balance of evidence and stating our own confidence in the conclusions, we outline several new questions that must now be addressed if this field is going to evolve into a predictive science that can help conserve and manage ecological processes in ecosystems.     

The functional significance of colouration in cetaceans

Cetaceans show many of the classic mammalian colouration patterns, such as uniform colouration, countershading, and prominent patches of colour, all within one relatively small taxon. We collated all the functional hypotheses for cetacean colouration that have been put forward in the literature and systematically tested them using comparative phylogenetic analyses. We found that countershading is a mechanism by which smaller cetacean species may avoid being seen by their prey. We discovered that prominent markings are associated with group living, fast swimming, and ostentatious behaviour at the surface, suggesting that they function in intraspecific communication. White markings on several parts of the body seem to be involved in the capture of fish, squid, and krill. Therefore, several different selection pressures have shaped the great diversity of skin colouration seen in extant cetaceans, although background matching, disruptive colouration and interspecific communication do not appear to be involved.     

The calpains: modular designs and functional diversity

The calpain family is named for the calcium dependence of the papain-like, thiol protease activity of the well-studied ubiquitous vertebrate enzymes calpain-1 (μ-calpain) and calpain-2 (m-calpain). Proteins showing sequence relatedness to the catalytic core domains of these enzymes are included in this ancient and diverse eukaryotic protein family. Calpains are examples of highly modular organization, with several varieties of amino-terminal or carboxy-terminal modules flanking a conserved core. Acquisition of the penta-EF-hand module involved in calcium binding (and the formation of heterodimers for some calpains) seems to be a relatively late event in calpain evolution. Several alternative mechanisms for binding calcium and associating with membranes/phospholipids are found throughout the family. The gene family is expanded in mammals, trypanosomes and ciliates, with up to 26 members in Tetrahymena, for example; in striking contrast to this, only a single calpain gene is present in many other protozoa and in plants. The many isoforms of calpain and their multiple splice variants complicate the discussion and analysis of the family, and challenge researchers to ascertain the relationships between calpain gene sequences, protein isoforms and their distinct or overlapping functions. In mammals and plants it is clear that a calpain plays an essential role in development. There is increasing evidence that ubiquitous calpains participate in a variety of signal transduction pathways and function in important cellular processes of life and death. In contrast to relatively promiscuous degradative proteases, calpains cleave only a restricted set of protein substrates and use complex substrate-recognition mechanisms, involving primary and secondary structural features of target proteins. The detailed physiological significance of both proteolytically active calpains and those lacking key catalytic residues requires further study.     

Characterization of a functional bacterial homologue of sodium-dependent neurotransmitter transporters

The tnaT gene of Symbiobacterium thermophilum encodes a protein homologous to sodium-dependent neurotransmitter transporters. Expression of the tnaT gene product in Escherichia coli conferred the ability to accumulate tryptophan from the medium and the ability to grow on tryptophan as a sole source of carbon. Transport was Na(+)-dependent and highly selective. The K(m) for tryptophan was approximately 145 nm, and tryptophan transport was unchanged in the presence of 100 microM concentrations of other amino acids. Tryptamine and serotonin were weak inhibitors with K(I) values of 200 and 440 microM, respectively. By using a T7 promoter-based system, TnaT with an N-terminal His(6) tag was expressed at high levels in the membrane and was purified to near-homogeneity in high yield.     

The mammalian centrosome and its functional significance

Primarily known for its role as major microtubule organizing center, the centrosome is increasingly being recognized for its functional significance in key cell cycle regulating events. We are now at the beginning of understanding the centrosome's functional complexities and its major impact on directing complex interactions and signal transduction cascades important for cell cycle regulation. The centrosome orchestrates entry into mitosis, anaphase onset, cytokinesis, G1/S transition, and monitors DNA damage. Recently, the centrosome has also been recognized as major docking station where regulatory complexes accumulate including kinases and phosphatases as well as numerous other cell cycle regulators that utilize the centrosome as platform to coordinate multiple cell cycle-specific functions. Vesicles that are translocated along microtubules to and away from centrosomes may also carry enzymes or substrates that use centrosomes as main docking station. The centrosome's role in various diseases has been recognized and a wealth of data has been accumulated linking dysfunctional centrosomes to cancer, Alstrom syndrome, various neurological disorders, and others. Centrosome abnormalities and dysfunctions have been associated with several types of infertility. The present review highlights the centrosome's significant roles in cell cycle events in somatic and reproductive cells and discusses centrosome abnormalities and implications in disease.     

The worldwide impact of urbanisation on avian functional diversity

Urbanisation is driving rapid declines in species richness and abundance worldwide, but the general implications for ecosystem function and services remain poorly understood. Here, we integrate global data on bird communities with comprehensive information on traits associated with ecological processes to show that assemblages in highly urbanised environments have substantially different functional composition and 20% less functional diversity on average than surrounding natural habitats. These changes occur without significant decreases in functional dissimilarity between species; instead, they are caused by a decrease in species richness and abundance evenness, leading to declines in functional redundancy. The reconfiguration and decline of native functional diversity in cities are not compensated by the presence of exotic species but are less severe under moderate levels of urbanisation. Thus, urbanisation has substantial negative impacts on functional diversity, potentially resulting in impaired provision of ecosystem services, but these impacts can be reduced by less intensive urbanisation practices.     

Biological significance of protease diversity

Probable stages of the development of enzymes of the hydrolase (protease) class, which resulted in enormous diversity of their modern forms, are considered. It is shown that complication of structural organization of these enzymes and mechanisms of their regulation in living cell promoted functional transformation of lowly selective catalysts of polypeptide destruction into highly specific regulators of biopolymer activity, biochemical pathways, and physiological processes. Undoubted interrelation of molecular evolution of proteases, complication of their repertoire, with certain historical stages in the development of the biosphere are revealed.     

The functional significance of aperture form in gastropods

Aperture form of marine prosobranch gastropods has evolved under the influence of a number of different selective forces, including: generation of shell form; protection from predation; accommodation of the foot during clamping behavior: and accommodation of water currents in and out of the mantle cavity. Aperture form correlates positively with foot shape in most gastropods and foot shape, in turn, correlates moderately well with substrate preference. Almost all gastropods that have non-round apertures elongate the aperture parallel to the foot so that water currenth tend to flow anteriorly to posteriorly. Fresh-water pulmonates have responded to somewhat different stresses. They exhibit clamping behavior and thus show correspondence between foot shape and aperture shape. They show less apertural strengthening as crab (or crayfish) predation is less of a factor and presumably because calcium carbonate is less available. They also lack anterior-posterior apertural elongation due to the absence of water currents through their mantle cavity. Due to the absence of mantle cavity water currents and clamping behavior, terrestrial gastropods do not show the apertural modifications associated with these two factors. In addition. few adaptations of apertural form are present to resist predation. Instead, many of the apertural modifications of terrestrial pulmonates seem to be concer-ned with the problems of water loss during estivation.     

The functional and phylogenetic significance of dinoflagellate eyespots

The eyespots or stigmas from five species of dinoflagellates fall into three distinct categories: independent eyespot which is not membrane bound; independent eyespot which is surrounded by three membranes; eyespot situated at the periphery of a chloroplast. In all cases the eyespot is situated behind the longitudinal groove or sulcus and there is a strand of microtubules between the eyespot and the cell covering or theca. In two cases the strand has been clearly shown to originate near the base of the longitudinal flagellum, which is the one passing over the eyespot and is also responsible for directional movement of the cell. The microtubular strand is presumed to play a part in the transmission of directional stimulation from eyespot to flagellum and a hypothesis is advanced to explain how this may be brought about. Phylogenetically, the structure of the various types of eyespots would link these dinoflagellates with euglenids and chrysophytes , and the diversity found in the dinoflagellates is probably a reflection of the diverse origin of chloroplasts in this group.