Follow the leader: preference for specific amino acids directly following the initial methionine in proteins of different organisms

It is well established that the vast majority of proteins of all taxonomical groups and species are initiated by an AUG codon, translated into the amino acid methionine (Met). Many attempts were made to evaluate the importance of the sequences surrounding the initiation codon, mostly focusing on the RNA sequence. However, the role and importance of the amino acids following the initiating Met residue were rarely investigated, mostly in bacteria and fungi. Herein, we computationally examined the protein sequences of all major taxonomical groups represented in the Swiss-Prot database, and evaluated the preference of each group to specific amino acids at the positions directly following the initial Met. The results indicate that there is a species-specific preference for the second amino acid of the majority of protein sequences. Interestingly, the preference for a certain amino acid at the second position changes throughout evolution from lysine in prokaryotes, through serine in lower eukaryotes, to alanine in higher plants and animals.     

Calling louder and longer: how bats use biosonar under severe acoustic interference from other bats

Active-sensing systems such as echolocation provide animals with distinct advantages in dark environments. For social animals, however, like many bat species, active sensing can present problems as well: when many individuals emit bio-sonar calls simultaneously, detecting and recognizing the faint echoes generated by one''s own calls amid the general cacophony of the group becomes challenging. This problem is often termed ‘jamming’ and bats have been hypothesized to solve it by shifting the spectral content of their calls to decrease the overlap with the jamming signals. We tested bats’ response in situations of extreme interference, mimicking a high density of bats. We played-back bat echolocation calls from multiple speakers, to jam flying Pipistrellus kuhlii bats, simulating a naturally occurring situation of many bats flying in proximity. We examined behavioural and echolocation parameters during search phase and target approach. Under severe interference, bats emitted calls of higher intensity and longer duration, and called more often. Slight spectral shifts were observed but they did not decrease the spectral overlap with jamming signals. We also found that pre-existing inter-individual spectral differences could allow self-call recognition. Results suggest that the bats’ response aimed to increase the signal-to-noise ratio and not to avoid spectral overlap.     

Active control of acoustic field-of-view in a biosonar system

Active-sensing systems abound in nature, but little is known about systematic strategies that are used by these systems to scan the environment. Here, we addressed this question by studying echolocating bats, animals that have the ability to point their biosonar beam to a confined region of space. We trained Egyptian fruit bats to land on a target, under conditions of varying levels of environmental complexity, and measured their echolocation and flight behavior. The bats modulated the intensity of their biosonar emissions, and the spatial region they sampled, in a task-dependant manner. We report here that Egyptian fruit bats selectively change the emission intensity and the angle between the beam axes of sequentially emitted clicks, according to the distance to the target, and depending on the level of environmental complexity. In so doing, they effectively adjusted the spatial sector sampled by a pair of clicks-the "field-of-view." We suggest that the exact point within the beam that is directed towards an object (e.g., the beam's peak, maximal slope, etc.) is influenced by three competing task demands: detection, localization, and angular scanning-where the third factor is modulated by field-of-view. Our results suggest that lingual echolocation (based on tongue clicks) is in fact much more sophisticated than previously believed. They also reveal a new parameter under active control in animal sonar-the angle between consecutive beams. Our findings suggest that acoustic scanning of space by mammals is highly flexible and modulated much more selectively than previously recognized.     

Big words, halved brains and small worlds: complex brain networks of figurative language comprehension

Language comprehension is a complex task that involves a wide network of brain regions. We used topological measures to qualify and quantify the functional connectivity of the networks used under various comprehension conditions. To that aim we developed a technique to represent functional networks based on EEG recordings, taking advantage of their excellent time resolution in order to capture the fast processes that occur during language comprehension. Networks were created by searching for a specific causal relation between areas, the negative feedback loop, which is ubiquitous in many systems. This method is a simple way to construct directed graphs using event-related activity, which can then be analyzed topologically. Brain activity was recorded while subjects read expressions of various types and indicated whether they found them meaningful. Slightly different functional networks were obtained for event-related activity evoked by each expression type. The differences reflect the special contribution of specific regions in each condition and the balance of hemispheric activity involved in comprehending different types of expressions and are consistent with the literature in the field. Our results indicate that representing event-related brain activity as a network using a simple temporal relation, such as the negative feedback loop, to indicate directional connectivity is a viable option for investigation which also derives new information about aspects not reflected in the classical methods for investigating brain activity.     

Nutritional status, cognition, and survival: a new role for leptin and AMP kinase

Although adequate nutrition is essential for optimal neural activity and survival, mild energy restriction may improve cognition and prolong longevity. Energy status is monitored by the cellular AMP-activated protein kinase (AMPK) system, whereas leptin regulates total energy balance. We investigated the roles of AMPK and leptin in cognition and survival under diet restriction (DR). Hippocampal AMPK activity increases with energy restriction. Modest activation (DR to 60%) induces neurogenesis and improves cognition. However, DR to 40% augmented AMPK activity, reduced cognition and catecholamines, and increased neural apoptosis and mortality. Leptin signaling is preserved only in DR to 60%, countering the effects of AMPK "overactivation" by preventing neuroapoptosis, restoring noradrenergic activity and behavioral performance, and increasing longevity. The balance between leptin and AMPK is crucial in determining neuronal fate, cognitive ability, and survival. Should these findings extend to Man, then controlled activation of AMPK may improve neurodegenerative diseases, and leptin may have a new role in treating stress-associated malnutrition.     

Mapping the DNA- and zinc-binding domains of ASR1 (abscisic acid stress ripening), an abiotic-stress regulated plant specific protein

Abscisic acid stress ripening (ASR1) is a highly charged low molecular weight plant specific protein that is regulated by salt- and water-stresses. The protein possesses a zinc-dependent DNA-binding activity (Kalifa et al., Biochem. J. 381 (2004) 373) and overexpression in transgenic plants results in an increased salt-tolerance (Kalifa et al., Plant Cell Environ. 27 (2004) 1459). There are no structure homologs of ASR1, thus the structural and functional domains of the protein cannot be predicted. Here, we map the protein domains involved in the binding of Zn(2+) and DNA. Using mild acid hydrolysis, and a series of ASR1 carboxy-terminal truncations we show that the zinc-dependent DNA-binding could be mapped to the central/carboxy-terminal domain. In addition, using MALDI-TOF-MS with a non-acidic matrix, we show that two zinc ions are bound to the amino-terminal domain. Other zinc ion(s) bind the DNA-binding domain. Binding of zinc to ASR1 induces conformational changes resulting in a decreased sensitivity to proteases.     

Anaerobic Ammonium-Oxidizing (Anammox) Bacteria and Associated Activity in Fixed-Film Biofilters of a Marine Recirculating Aquaculture System

Microbial communities in the biological filter and waste sludge compartments of a marine recirculating aquaculture system were examined to determine the presence and activity of anaerobic ammonium-oxidizing (anammox) bacteria. Community DNA was extracted from aerobic and anaerobic fixed-film biofilters and the anaerobic sludge waste collection tank and was analyzed by amplifying 16S rRNA genes by PCR using anammox-selective and universal GC-clamped primers. Separation of amplified PCR products by denaturing gradient gel electrophoresis and sequencing of the different phylotypes revealed a diverse biofilter microbial community. While Planctomycetales were found in all three communities, the anaerobic denitrifying biofilters contained one clone that exhibited high levels of sequence similarity to known anammox bacteria. Fluorescence in situ hybridization studies using an anammox-specific probe confirmed the presence of anammox Planctomycetales in the microbial biofilm from the denitrifying biofilters, and anammox activity was observed in these biofilters, as detected by the ability to simultaneously consume ammonia and nitrite. To our knowledge, this is the first identification of anammox-related sequences in a marine recirculating aquaculture filtration system, and our findings provide a foundation for incorporating this important pathway for complete nitrogen removal in such systems.     

AMPK activation regulates apoptosis, adipogenesis, and lipolysis by eIF2alpha in adipocytes

AMP-activated protein kinase (AMPK) is a metabolic master switch regulating glucose and lipid metabolism. Recently, AMPK has been implicated in the control of adipose tissue content. Yet, the nature of this action is controversial. We examined the effect on F442a adipocytes of the AMPK activator-AICAR. Activation of AMPK induced dose-dependent apoptotic cell death, inhibition of lipolysis, and downregulatation key adipogenic genes, such as peroxisome proliferator-activated receptor (PPARgamma) and CCAAT/enhancer-binding protein alpha (C/EBPalpha). We have identified the alpha-subunit of the eukaryotic initiation factor-2 (eIF2alpha) as a target gene which is phosphorylated following AICAR treatment. Such phosphorylation is one of the best-characterized mechanisms for downregulating protein synthesis. 2-Aminopurine (2-AP), an inhibitor of eIF2alpha kinases, could overcome the apoptotic effect of AICAR, abolishing the reduction of PPARgamma and C/EBPalpha and the lipolytic properties of AMPK. Thus, AMPK may diminish adiposity via reduction of fat cell number through eIF2alpha-dependent translation shutdown.     

Colored shading nets impede insect invasion and decrease the incidences of insect‐transmitted viral diseases in vegetable crops

Black shading nets are commonly used to protect agricultural crops from excessive solar radiation and wind, and for water saving. Recent studies have demonstrated that when black nets were replaced by either red, yellow, or pearl nets (ChromatiNets^?) of equivalent shading capacity, it increased the fruit yield and improved the quality of bell peppers (Capsicum annuum L.) and tomatoes (Solanum lycopersicum L.) (both Solanaceae). We studied the effects of these colored shading nets on the infestation by aphids [Myzus persicae (Sulzer) and Aphis gossypii Glover (both Hemiptera: Aphididae)] and whiteflies [Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae)], and the incidence of the viral diseases transmitted by these insects, for five consecutive years (2006–2010). These studies were conducted in the semi‐arid Besor region in southern Israel. The plants were grown in ‘walk‐in’ tunnels that were covered by several nets of 35% shading capacity in the range of photosynthetically active radiation. Although the shading nets permit free passage of these pests, the infestation levels of aphids and whiteflies in tunnels covered by either the yellow or pearl nets were consistently 2–3× lower than in tunnels covered by the black or red nets. In accordance with the pest results, when the incidences of Cucumber mosaic virus in pepper grown under the black or red nets ranged between 35 and 89%, they were 2–10× lower under the yellow or pearl nets. Similarly, when the incidences of necrotic Potato virus Y in tomato grown under black or red nets ranged between 42 and 50%, they were 2–3× lower under the yellow or pearl nets. Also, when the incidences of Tomato yellow leaf curl virus in tomato grown under the black or red nets ranged between 15 and 50%, but they were 2–4× lower under the yellow or pearl nets. Putative mechanisms of crop protection achieved by the yellow and pearl nets are discussed.     

Migration, coherence and persistence in a fragmented landscape

The chance of local extinction is high during periods of small population size. Accordingly, a metapopulation made of local communities that support internal population cycling may face the threat of regional extinction if the local dynamics is coherent (synchronized). These systems achieve maximum sustainability at an intermediate level of migration that allows recolonization but prevents synchronization. Here we implement an individual-based simulation technique to examine the maximum persistence condition for a system of patch habitats connected by passive migration. The models discussed in this paper take into consideration realistic elements of metapopulations, such as migration cost, disordered spatial structure, frustration and environmental noise. It turns out that the state with maximum anti-correlation between neighboring patches is the most sustainable one, even in the presence of these complications. The results suggest, at least for small systems, a model independent conservation strategy: coherence between neighboring local communities has, in general, a negative impact, and population will benefit from intervention that increases anti-correlations.