The impact of a fox‐ and cat‐free safe haven on the bird fauna of remnant vegetation in southwestern Australia

Introduced predators are a serious threat to Australian vertebrates. However, the consequences of predation for an area's avifauna have rarely been quantified. We took advantage of the establishment of a 7,832 ha fox‐ and cat‐free safe haven at Mt Gibson, in Western Australia, to assess the consequences of excluding introduced mammal predators on the bird fauna. Bird surveys were conducted over 6 years, before and after the establishment of the introduced predator‐free safe haven. After 3 years, half the sites were enclosed by the fence that excluded introduced predators, while the remainder of sites remained outside the fence and were exposed to fox and cat activity. The sites were stratified by four major vegetation types. A total of 91 bird species were variously detectable with the survey approach, but were typically more detectable during morning surveys. Site occupancy varied considerably among species, but overall, occupancy by all species was most likely to be either not impacted or positively impacted by the safe haven. The most notable change was that avifaunal richness appeared to increase in woodland and shrubland habitats within, as compared to outside, the safe haven. We conclude that: (1) the safe haven had an overall positive impact on bird occupancy; and (2) there were no consistent trends with respect to the kinds of species whose occupancy was positively impacted, beyond them all being small‐ to medium‐sized birds and mostly insectivorous. However, these conclusions must be tempered by the poor detection probability of many species.     

Protein kinase D1 inhibition interferes with mitosis progression

Protein kinase D1 (PKD1) plays a vital role in signal transduction, cell proliferation, membrane trafficking, and cancer; however, the majority of the studies up to date had centered primarily on PKD1 functions in interphase, very little is known about its role during cell division. We previously demonstrated that during mitosis PKD1 is activated and associated with centrosomes, spindles, and midbodies. However, these observations did not address whether PKD1 was associated with mitosis regulation. Accordingly, we used rapidly acting PKD-specific inhibitors to examine the contribution of PKD1 the sequence of events in mitosis. We found that although PKD1 overexpression did not affect mitosis progression, suppression of its catalytic activity by two structurally unrelated inhibitors (kb NB 142-70 and CRT 0066101) induced a significant delay in metaphase to anaphase transition time. PKD1 inhibition during mitosis also produced the appearance of abnormal spindles, defects in chromosome alignment, and segregation as well as apoptosis. Thus, these observations indicate that PKD1 activity is associated with mitosis regulation.     

Sex determination of buffalo embryos (Bubalus bubalis) by polymerase chain reaction

The aim of this study was to identify a simple, rapid method for sex determination of in vitro produced buffalo embryos, amplifying Y-chromosome-specific repeat sequences by polymerase chain reaction (PCR). Buffalo oocytes collected from slaughtered animals were matured, fertilised and cultured in vitro for 7 days. On day 7 embryos were evaluated and divided in to six groups according to developmental stage (2, 4, 8, 16 cells, morulae and blastocyst). Each embryo was stored singly in phosphate-buffered saline at -20 degrees C until PCR. Two different methods of extraction of DNA were compared: a standard procedure (ST), using a normal extraction by phenol-chloroform, isoamyl alcohol and final precipitation in absolute ethanol and a direct procedure (DT), using a commercial kit (Qiaquik-Qiagen mini blood). A pair of bovine satellite primers and two pairs of different bovine Y-chromosome-specific primers (BRY4.a and BRY.1) were used in the PCR assay on embryos and on whole blood samples collected from male and female adult buffaloes, used as control. The trial was carried out on 359 embryos (193 for ST and 166 for DT). When DNA samples from blood were amplified, the sex determined by PCR always corresponded to the anatomical sex. Embryo sexing was not possible in two embryos in ST and one embryo in DT. Both extraction protocols recovered sufficient quantities of target DNA at all developmental stages, but the time required for the ST (24 h) limits its use in embryo sexing and supports the use of commercial extraction kits (5 h).     

Differential Regulation and Function of CD73, a Glycosyl-Phosphatidylinositol–linked 70-kD Adhesion Molecule, on Lymphocytes and Endothelial Cells

CD73, otherwise known as ecto-5′-nucleotidase, is a glycosyl-phosphatidylinositol–linked 70-kD molecule expressed on different cell types, including vascular endothelial cells (EC) and certain subtypes of lymphocytes. There is strong evidence for lymphocyte CD73 having a role in several immunological phenomena such as lymphocyte activation, proliferation, and adhesion to endothelium, but the physiological role of CD73 in other cell types is less clear. To compare the biological characteristics of CD73 in different cell types, we have studied the structure, function, and surface modulation of CD73 on lymphocytes and EC. CD73 molecules on lymphocytes are shed from the cell surface as a consequence of triggering with an antiCD73 mAb, mimicking ligand binding. In contrast, triggering of endothelial CD73 does not have any effect on its expression. Lymphocyte CD73 is susceptible to phosphatidylinositol phospholipase, whereas only a small portion of CD73 on EC could be removed by this enzyme. Furthermore, CD73 on EC was unable to deliver a tyrosine phosphorylation inducing signal upon mAb triggering, whereas triggering of lymphocyte CD73 can induce tyrosine phosphorylation. Despite the functional differences, CD73 molecules on lymphocytes and EC were practically identical structurally, when studied at the protein, mRNA, and cDNA level. Thus, CD73 is an interesting example of a molecule which lacks structural variants but yet has a wide diversity of biological functions. We suggest that the ligand- induced shedding of lymphocyte CD73 represents an important and novel means of controlling lymphocyte– EC interactions.     

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

Inferring gene co-expression networks is a useful process for understanding gene regulation and pathway activity. The networks are usually undirected graphs where genes are represented as nodes and an edge represents a significant co-expression relationship. When expression data of multiple (p) genes in multiple (K) conditions (e.g., treatments, tissues, strains) are available, joint estimation of networks harnessing shared information across them can significantly increase the power of analysis. In addition, examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. Condition adaptive fused graphical lasso (CFGL) is an existing method that incorporates condition specificity in a fused graphical lasso (FGL) model for estimating multiple co-expression networks. However, with computational complexity of O(p²K log K), the current implementation of CFGL is prohibitively slow even for a moderate number of genes and can only be used for a maximum of three conditions. In this paper, we propose a faster alternative of CFGL named rapid condition adaptive fused graphical lasso (RCFGL). In RCFGL, we incorporate the condition specificity into another popular model for joint network estimation, known as fused multiple graphical lasso (FMGL). We use a more efficient algorithm in the iterative steps compared to CFGL, enabling faster computation with complexity of O(p²K) and making it easily generalizable for more than three conditions. We also present a novel screening rule to determine if the full network estimation problem can be broken down into estimation of smaller disjoint sub-networks, thereby reducing the complexity further. We demonstrate the computational advantage and superior performance of our method compared to two non-condition adaptive methods, FGL and FMGL, and one condition adaptive method, CFGL in both simulation study and real data analysis. We used RCFGL to jointly estimate the gene co-expression networks in different brain regions (conditions) using a cohort of heterogeneous stock rats. We also provide an accommodating C and Python based package that implements RCFGL.     

Synaptophysin I selectively specifies the exocytic pathway of synaptobrevin 2/VAMP2

Biogenesis and recycling of synaptic vesicles are accompanied by sorting processes that preserve the molecular composition of the compartments involved. In the present study, we have addressed the targeting of synaptobrevin 2/VAMP2 (vesicle-associated membrane protein 2), a critical component of the synaptic vesicle--fusion machinery, in a heterotypic context where its sorting is not confounded by the presence of other neuron-specific molecules. Ectopically expressed synaptophysin I interacts with VAMP2 and alters its default surface targeting to a prominent vesicular distribution, with no effect on the targeting of other membrane proteins. Protein-protein interaction is not sufficient for the control of VAMP2 sorting, which is mediated by the C-terminal domain of synaptophysin I. Synaptophysin I directs the sorting of VAMP2 to vesicles before surface delivery, without influencing VAMP2 endocytosis. Consistent with this, dynamin and alpha-SNAP (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein) mutants which block trafficking at the plasma membrane do not abrogate the effect of synaptophysin I on VAMP2 sorting. These results indicate that the sorting determinants of synaptic vesicle proteins can operate independently of a neuronal context and implicate the association of VAMP2 with synaptophysin I in the specification of the pathway of synaptic vesicle biogenesis.     

Bacterial colonization of a fumigated alkaline saline soil

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m^?1, and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8 %) compared to the unfumigated soil (34.2 %), while that of the Bacteroidetes decreased from 16.2 % in the unfumigated soil to 8.8 % in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7 % in the unfumigated soil to 25.7 %. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.     

Rethinking the dispersal of Homo sapiens out of Africa

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.