An “orientation sphere” visualization for examining animal head movements

1. Animal behavior is elicited, in part, in response to external conditions, but understanding how animals perceive the environment and make the decisions that bring about these behavioral responses is challenging.
2. Animal heads often move during specific behaviors and, additionally, typically have sensory systems (notably vision, smell, and hearing) sampling in defined arcs (normally to the front of their heads). As such, head‐mounted electronic sensors consisting of accelerometers and magnetometers, which can be used to determine the movement and directionality of animal heads (where head “movement” is defined here as changes in heading [azimuth] and/or pitch [elevation angle]), can potentially provide information both on behaviors in general and also clarify which parts of the environment the animals might be prioritizing (“environmental framing”).
3. We propose a new approach to visualize the data of such head‐mounted tags that combines the instantaneous outputs of head heading and pitch in a single intuitive spherical plot. This sphere has magnetic heading denoted by “longitude” position and head pitch by “latitude” on this “orientation sphere” (O‐sphere).
4. We construct the O‐sphere for the head rotations of a number of vertebrates with contrasting body shape and ecology (oryx, sheep, tortoises, and turtles), illustrating various behaviors, including foraging, walking, and environmental scanning. We also propose correcting head orientations for body orientations to highlight specific heading‐independent head rotation, and propose the derivation of O‐sphere‐metrics, such as angular speed across the sphere. This should help identify the functions of various head behaviors.
5. Visualizations of the O‐sphere provide an intuitive representation of animal behavior manifest via head orientation and rotation. This has ramifications for quantifying and understanding behaviors ranging from navigation through vigilance to feeding and, when used in tandem with body movement, should provide an important link between perception of the environment and response to it in free‐ranging animals.

     

A preliminary survey on the occurrence of mycotoxigenic fungi and mycotoxins contaminating red rice at consumer level in Selangor, Malaysia

Red rice is a fermented product of Monascus spp. It is widely consumed by Malaysian Chinese who believe in its pharmacological properties. The traditional method of red rice preparation disregards safety regulation and renders red rice susceptible to fungal infestation and mycotoxin contamination. A preliminary study was undertaken aiming to determine the occurrence of mycotoxigenic fungi and mycotoxins contamination on red rice at consumer level in Selangor, Malaysia. Fifty red rice samples were obtained and subjected to fungal isolation, enumeration, and identification. Citrinin, aflatoxin, and ochratoxin-A were quantitated by ELISA based on the presence of predominant causal fungi. Fungal loads of 1.4?×?10⁴ to 2.1?×?10⁶?CFU/g exceeded Malaysian limits. Monascus spp. as starter fungi were present in 50 samples (100 %), followed by Penicillium chrysogenum (62 %), Aspergillus niger (54 %), and Aspergillus flavus (44 %). Citrinin was present in 100 % samples (0.23–20.65 mg/kg), aflatoxin in 92 % samples (0.61–77.33 μg/kg) and Ochratoxin-A in 100 % samples (0.23–2.48 μg/kg); 100 % citrinin and 76.09 % aflatoxin exceeded Malaysian limits. The presence of mycotoxigenic fungi served as an indicator of mycotoxins contamination and might imply improper production, handling, transportation, and storage of red rice. Further confirmatory analysis (e.g., HPLC) is required to verify the mycotoxins level in red rice samples and to validate the safety status of red rice.     

Fusarium Species Associated with Mango Malformation in Peninsular Malaysia

Mango malformation has become the most important global disease on mango. Fusarium species previously associated with this disease include F. mangiferae, F. mexicanum, F. sterilihyphosum, F. proliferatum, F. subglutinans and F. tupiense. A few strains of F. proliferatum have been reported from Malaysia, but in this study, we report the results of more extensive sampling. The recovered strains were evaluated with morphology, mating tester strain cross‐fertility, amplified fragment length polymorphisms (AFLPs), and partial DNA sequences of the genes encoding translation elongation factor 1‐α (tef‐1α) and β‐tubulin (tub‐2). Amongst the 43 strains evaluated, three species were identified – F. proliferatum, F. mangiferae and F. subglutinans – with F. proliferatum being the most frequent (69%). None of the Fusarium species that appear to originate in the Americas were recovered in Malaysia, which suggests special measures may be warranted to keep these species from entering the country.     

Resilience of a forest fragment exposed to long-term isolation in Singapore

Background: Fragmentation can fundamentally alter the structure of tropical forests. However, the impacts of fragmentation may vary significantly among regions and lead to different outcomes.

Aims: We examined the structure, composition and dynamics of a forest fragment in Singapore to investigate reasons for the apparent resilience of this forest to long-term isolation.

Methods: We conducted 5 censuses of 12,688 trees ≥1-cm dbh in a 2-ha plot on the edge of the fragment between 1993 and 2012.

Results: Stem density and basal area were not significantly different between 1993 and 2012 and were typical of other south-east Asian forests. However, there were short-term decreases in both variables after droughts in 1997 and 2009, both followed by recovery. Total mortality rate over the 19 years was 3.3% year^?1, considerably higher than other tropical forests in Asia, but it was balanced by high recruitment. The 10 most abundant species were primary forest species, pioneer species comprised <5% of all stems, and none of the 338 species in the plot was exotic. However, species abundances changed more than expected by chance for 86 species, and the rank order of the commonest species changed significantly. Species abundance changes were not related to known species traits.

Conclusions: Despite the long period of isolation, we found a surprising level of resilience of the Bukit Timah forest. While the forest may be more sensitive to the effects of climatic fluctuations at decadal time scales, there were very few signs of forest degradation in this diverse fragment of tropical forest.     

Mathematical modeling of cell growth in a 3D scaffold and validation of static and dynamic cultures

Tissue engineering, an immensely important field in contemporary clinical practices, aims at the repair or replacement of damaged tissues. The mathematical model proposed herein shows the distribution and growth of cells in their characteristic time in a 3D scaffold model. This study contributes to the progress of simulation techniques in static and dynamic cultures of bone tissue. Brinkman, nutrient transport, and cell growth equations are brought together to quantify the growth behavior of cells. However, when a static culture is being studied, the Brinkman equation is eliminated. The model was validated by experimental cell culture using 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay and scanning electron microscopy. Then, static and dynamic cultures were compared to assess the cell density and cell distribution in the scaffold. Cell counting after 21 days of cell culture showed that the number of cells increased 42‐fold in static and 53.5‐fold in dynamic cultures, which was in good agreement with our model estimations (37‐fold increase in the number of cells in static and 49‐fold increase in dynamic cultures). In conclusion, our mathematical model could predict cell distribution and growth in the scaffold.     

Effects of two weeks' mandatory snack consumption on energy intake and energy balance

Objective: Our goal was to compare the effects of mandatory consumption of commercial snack products (CSPs) on energy intakes and energy balance in free‐living adults and to assess the interaction between habitual level of CSP consumption and the interventions. Research Methods and Procedures: Four groups of 18 subjects (lean and overweight, males and females) were studied using a crossover design. Subjects consumed one type of CSP (high‐carbohydrate, high‐fat, or mixed composition) at three manipulations of energy 0 MJ (control), 1.5 MJ (low‐energy), and 3.0 MJ (high‐energy) each day during three 14‐day interventions. The study design was parallel for type of CSP (macronutrient composition) and within‐subjects for energy level. Subjects self‐recorded food intakes between Days 8 and 14, and body weights were investigator‐recorded on Days 1, 8, and 15 of each intervention period. Daily energy expenditure was estimated by heart rate monitoring. Results: Daily energy intakes increased from 10.4 MJ (control) to 11.1 MJ (low‐energy) and 11.5 MJ (high‐energy) (p < 0.001), resulting in a trend (not significant) for body weight gain. Energy balance was more positive when subjects were not recording their food intakes than when they were (p < 0.001). There was a trend (not significant) for greater increases in energy intake with increasing fat content, and energy density, of the interventions. Frequent CSP consumers compensated more for the interventions than did infrequent CSP consumers (R² = 0.125, p = 0.003). Discussion: Subjects partially compensated for energy when supplemented with CSPs over 14‐day periods, although this was insufficient to prevent some increase in energy balance. The level of compensation correlated with habitual energy intake from CSPs.     

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These fungi use extracellular oxidative enzymes that are also able to transform related aromatic compounds found in explosive contaminants, pesticides and toxic waste. We have sequenced the 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using a whole genome shotgun approach. The P. chrysosporium genome reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay. Analysis of the genome data will enhance our understanding of lignocellulose degradation, a pivotal process in the global carbon cycle, and provide a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching. This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens.     

Ethnic variation in tyrosinase and TYRP1 expression in photoexposed and photoprotected human skin

The relative expression of a number of key mediators of human pigmentation including tyrosinase, tyrosinase related protein-1 (TYRP1), endothelin-1 and adrenocorticotrophic hormone (ACTH) proteins were analysed and quantified in immunohistochemically stained skin sections using semiquantitative computer assisted image analysis. Comparisons were made between a range of different ethnic skin types including European, Chinese, Mexican, Indian and African at both chronically photoexposed and photoprotected sites. Melanocyte number varied little with ethnicity except in the European group which had 60-80% more melanocytes than other skin types (P < 0.01, n = 10; Student Neuman-Keuls). However, melanocyte number was increased approximately twofold in chronically photoexposed skin of all ethnic groups (P < 0.001, n = 48; paired t-test). Tyrosinase protein expression in melanocytes did not vary with ethnicity, but TYRP1 protein was significantly elevated (approximately 2.6-fold) in darkly pigmented African and Indian skin types compared with lightly pigmented Mexican, Chinese and European skin types. In melanocytes from chronically photoexposed skin, there was a modest but significant increase in the expression of tyrosinase protein (approximately 1.2-fold, P < 0.001, n = 48; paired t-test), together with a significant and slightly larger increase in the expression of TYRP1 protein (approximately 1.6-fold, P < 0.005, n = 48; paired t-test). In contrast, the expression of endothelin-1 and ACTH showed no significant variation with either ethnicity or photoexposure. These data are consistent with the view that maintenance of a chronically hyperpigmented phenotype in chronically photoexposed human skin is largely the result of a stable increase in the number of tyrosinase positive melanocytes at these sites. Moreover, the observed ethnic variation in TYRP1 protein expression suggests that TYRP1 may play a significant role in mediating ethnic differences in melanogenesis and constitutive skin pigmentation in vivo.     

Novel aminopeptidase specific for glycine from Actinomucor elegans

Glycyl aminopeptidase was purified 600-fold from a cell extract of Actinomucor elegans by ammonium sulfate fractionation and sequential chromatography on DEAE-Toyopearl, Toyopearl HW65C, and FPLC-Superdex 200 HR, with recovery of 3.3% of the activity. The enzyme highly specifically hydrolyzed Gly-X (amino acid, peptide, or arylamide) bonds. The enzyme hydrolyzed other amino acid residues but at a rate of less than one fifth that with Gly. The order was Gly > Ala > Met > Arg > Ser > Leu. The Km value for glycyl-2-naphthylamide was 0.24 mM. The enzyme was most active at pH 8.0 with glycyl-2-naphthylamide as the substrate and its optimal temperature was 40 degrees C. The enzyme was inhibited by iodoacetic acid, and p-chloromercuribenzoate but not done by diisopropylfluorophosphate, o-phenanthroline, or EDTA. Magnesium and calcium had no effect on enzymic activity, but the activity was suppressed by cadmium, zinc, and copper ions. The molecular mass was estimated to be 320 kDa by gel filtration on FPLC-Superdex 200 HR and 56.5 kDa by SDS-PAGE, so the enzyme probably was a hexamer.