Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata

<b>BACKGROUND</b>: Little is known about how apicomplexan parasites have evolved to infect different host species and cell types. Theileria annulata and Theileria parva invade and transform bovine leukocytes but each species favours a different host cell lineage. Parasite-encoded proteins secreted from the intracellular macroschizont stage within the leukocyte represent a critical interface between host and pathogen systems. Genome sequencing has revealed that several Theileria-specific gene families encoding secreted proteins are positively selected at the inter-species level, indicating diversification between the species. We extend this analysis to the intra-species level, focusing on allelic diversity of two major secretome families. These families represent a well-characterised group of genes implicated in control of the host cell phenotype and a gene family of unknown function. To gain further insight into their evolution and function, this study investigates whether representative genes of these two families are diversifying or constrained within the T. annulata population. <b>RESULTS</b>: Strong evidence is provided that the sub-telomerically encoded SVSP family and the host-nucleus targeted TashAT family have evolved under contrasting pressures within natural T. annulata populations. SVSP genes were found to possess atypical codon usage and be evolving neutrally, with high levels of nucleotide substitutions and multiple indels. No evidence of geographical sub-structuring of allelic sequences was found. In contrast, TashAT family genes, implicated in control of host cell gene expression, are strongly conserved at the protein level and geographically sub-structured allelic sequences were identified among Tunisian and Turkish isolates. Although different copy numbers of DNA binding motifs were identified in alleles of TashAT proteins, motif periodicity was strongly maintained, implying conserved functional activity of these sites. <b>CONCLUSIONS</b>: This analysis provides evidence that two distinct secretome genes families have evolved under contrasting selective pressures. The data supports current hypotheses regarding the biological role of TashAT family proteins in the management of host cell phenotype that may have evolved to allow adaptation of T. annulata to a specific host cell lineage. We provide new evidence of extensive allelic diversity in representative members of the enigmatic SVSP gene family, which supports a putative role for the encoded products in subversion of the host immune response

False killer whale dorsal fin disfigurements as a possible indicator of long-line fishery interactions in Hawaiian Waters

Scarring resulting from entanglement in fishing gear can be used to examine cetacean fishery interactions. False killer whales (Pseudorca crassidens) are known to interact with the Hawai'i-based tuna and swordfish long-line fishery in offshore Hawaiian waters. We examined the rate of major dorsal fin disfigurements of false killer whales from nearshore waters around the main Hawaiian Islands to assess the likelihood that individuals around the main islands are part of the same population that interacts with the fishery. False killer whales were encountered on 11 occasions between 2000 and 2004, and 80 distinctive individuals were photographically documented. Three of these (3.75%) had major dorsal fin disfigurements (two with the fins completely bent over and one missing the fin). Information from other research suggests that the rate of such disfigurements for our study population may be more than four times greater than for other odontocete populations. We suggest that the most likely cause of such disfigurements is interactions with longlines and that false killer whales found in nearshore waters around the main Hawaiian Islands are part of the same population that interacts with the fishery. Two of the animals documented with disfigurements had infants in close attendance and were thought to be adult females. This implies that even with such injuries, at least some females may be able to produce offspring, despite the importance of the dorsal fin in reproductive thermoregulation

Development and Composition of the Warty Layer in Balsam Fir. I. Development

The deposition and ultrastructure of the warty layer in developing tracheids of balsam fir [Abies balsamea (L.) Mill.] were studied by means of transmission electron microscopy. The wart structure gradually was developed external to the plasma membrane after secondary wall deposition and the greater part of lignification were complete. Warts were synthesized first in the cell corners and pit cavities and then on the remainder of the cell walls. No cytoplasmic organelle was found to be associated specifically with wart formation. After the warty layer was elaborated, the cytoplasm disappeared from the cell, leaving no discernible trace of disorganized residue. The bulk of the wart structure exhibited staining properties similar to those of lignin. However, the basal portions of individual warts were sometimes less darkly stained than the outer portions, indicating possible heterogeneous composition

Development and Composition of the Warty Layer in Balsam Fir. II. Composition

From its response to various chemical, physical, fungal, and enzymatic treatments, it was concluded that the warty layer in balsam fir consisted largely of a ligninlike material that was visibly more resistant to extraction than a large fraction of other lignin in the fiber cell wall. Since the warts were the cell-wall component most accessible to the treatment solutions, it is probable that the material in the warty layer was more concentrated and condensed than lignin in other parts of the wall. Vacuum drying at 105 C appeared to condense the wart structure still further, making it even more resistant to most treatments. Gel filtration indicated that the warty layer was extracted as a high molecular weight material by certain treatments. The warty layer may act as a barrier that slows the penetration of liquids into the cell wall and thereby may cause different rates of delignification for different wood species. The basal component of individual warts and some of the accompanying encrustant on the inner surface of the cell wall were found to contain an amorphous carbohydrate, probably a pentosan or a pectic substance. Attempts at physical isolation of the warts were largely unsuccessful

Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands

Sequence-specific DNA-binding small molecules that can permeate human cells potentially could regulate transcription of specific genes. Multiple cellular DNA-binding transcription factors are required by HIV type 1 for RNA synthesis. Two pyrrole-imidazole polyamides were designed to bind DNA sequences immediately adjacent to binding sites for the transcription factors Ets-l, lymphoid-enhancer binding factor 1, and TATA-box binding protein. These synthetic ligands specifically inhibit DNA-binding of each transcription factor and HIV type 1 transcription in cell-free assays. When used in combination, the polyamides inhibit virus replication by >99% in isolated human peripheral blood lymphocytes, with no detectable cell toxicity, The ability of small molecules to target predetermined DNA sequences located within RNA polymerase II promoters suggests a general approach for regulation of gene expression, as well as a mechanism for the inhibition of viral replication

Supporting public involvement in interview and other panels: a systematic review.

BACKGROUND: Members of the public are increasingly being invited to become members of a variety of different panels and boards. OBJECTIVE: This study aimed to systematically search the literature to identify studies relating to support or training provided to members of the public who are asked to be members of an interview panel. SEARCH STRATEGY: A systematic search for published and unpublished studies was carried out from June to September 2015. The search methods included electronic database searching, reference list screening, citation searching and scrutinizing online sources. INCLUSION CRITERIA: We included studies of any design including published and unpublished documents which outlined preparation or guidance relating to public participants who were members of interview panels or representatives on other types of panels or committees. DATA SYNTHESIS: Results were synthesised via narrative methods. MAIN RESULTS: Thirty-six documents were included in the review. Scrutiny of this literature highlighted ten areas which require consideration when including members of the public on interview panels: financial resources; clarity of role; role in the interview process; role in evaluation; training; orientation/induction; information needs; terminology; support; and other public representative needs such as timing, accessibility and support with information technology. DISCUSSION AND CONCLUSIONS: The results of the review emphasize a range of elements that need to be fully considered when planning the involvement of public participants on interview panels. It highlights potential issues relating to the degree of involvement of public representatives in evaluating/grading decisions and the need for preparation and on-going support

Semigroup Closures of Finite Rank Symmetric Inverse Semigroups

We introduce the notion of semigroup with a tight ideal series and investigate their closures in semitopological semigroups, particularly inverse semigroups with continuous inversion. As a corollary we show that the symmetric inverse semigroup of finite transformations $\mathscr{I}_\lambda^n$ of the rank $\leqslant n$ is algebraically closed in the class of (semi)topological inverse semigroups with continuous inversion. We also derive related results about the nonexistence of (partial) compactifications of classes of semigroups that we consider.Comment: With the participation of the new coauthor - Jimmie Lawson - the manuscript has been substantially revised and expanded. Accordingly, we have also changed the manuscript titl

Syzygies in equivariant cohomology for non-abelian Lie groups

We extend the work of Allday-Franz-Puppe on syzygies in equivariant cohomology from tori to arbitrary compact connected Lie groups G. In particular, we show that for a compact orientable G-manifold X the analogue of the Chang-Skjelbred sequence is exact if and only if the equivariant cohomology of X is reflexive, if and only if the equivariant Poincare pairing for X is perfect. Along the way we establish that the equivariant cohomology modules arising from the orbit filtration of X are Cohen-Macaulay. We allow singular spaces and introduce a Cartan model for their equivariant cohomology. We also develop a criterion for the finiteness of the number of infinitesimal orbit types of a G-manifold.Comment: 28 pages; minor change

Acoustic differentiation of Shiho- and Naisa-type short-finned pilot whales in the Pacific Ocean

Author Posting. © Acoustical Society of America, 2017. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 114 (2017): 737–748, doi: 10.1121/1.4974858.Divergence in acoustic signals used by different populations of marine mammals can be caused by a variety of environmental, hereditary, or social factors, and can indicate isolation between those populations. Two types of genetically and morphologically distinct short-finned pilot whales, called the Naisa- and Shiho-types when first described off Japan, have been identified in the Pacific Ocean. Acoustic differentiation between these types would support their designation as sub-species or species, and improve the understanding of their distribution in areas where genetic samples are difficult to obtain. Calls from two regions representing the two types were analyzed using 24 recordings from Hawai‘i (Naisa-type) and 12 recordings from the eastern Pacific Ocean (Shiho-type). Calls from the two types were significantly differentiated in median start frequency, frequency range, and duration, and were significantly differentiated in the cumulative distribution of start frequency, frequency range, and duration. Gaussian mixture models were used to classify calls from the two different regions with 74% accuracy, which was significantly greater than chance. The results of these analyses indicate that the two types are acoustically distinct, which supports the hypothesis that the two types may be separate sub-species.Funding for Hawaiian data collection was provided by grants from the Pacific Islands Fisheries Science Center and Office of Naval Research, as well as Commander, Pacific Fleet. The SoundTrap was purchased with funding from the Scripps Institution of Oceanography/National Science Foundation Interdisciplinary Graduate Education in Research Techniques fellowship program. DMON data collection and portions of the analysis were funded by the Office of Naval Research [Grant Nos. N000141110612 (T.A.M. and R.W.B.) and N00014-15-1-2299 (M.A.R.); Program Manager Michael J. Weise], and WHOI Marine Mammal Center and the Sawyer and Penzance Endowed Funds to T.A.M