Looking and homing: how displaced ants decide where to go

We caught solitary foragers of the Australian Jack Jumper ant, Myrmecia croslandi, and released them in three compass directions at distances of 10 and 15 m from the nest at locations they have never been before. We recorded the head orientation and the movements of ants within a radius of 20 cm from the release point and, in some cases, tracked their subsequent paths with a differential GPS. We find that upon surfacing from their transport vials onto a release platform, most ants move into the home direction after looking around briefly. The ants use a systematic scanning procedure, consisting of saccadic head and body rotations that sweep gaze across the scene with an average angular velocity of 90° s⁻¹ and intermittent changes in turning direction. By mapping the ants’ gaze directions onto the local panorama, we find that neither the ants’ gaze nor their decisions to change turning direction are clearly associated with salient or significant features in the scene. Instead, the ants look most frequently in the home direction and start walking fast when doing so. Displaced ants can thus identify home direction with little translation, but exclusively through rotational scanning. We discuss the navigational information content of the ants’ habitat and how the insects’ behaviour informs us about how they may acquire and retrieve that information.     

Abundant alkali-sensitive sites in DNA of human and mouse sperm

The DNA of human and mouse sperm cells was analyzed by single-cell microgel electrophoresis, by agarose gel electrophoresis, and by alkaline elution--three techniques that can detect single-strand DNA breaks and/or labile sites. Under these conditions a surprisingly large number of single-strand DNA breaks, approximately 10(6) to 10(7) per genome, were detected in human and mouse sperm but not in human lymphocytes or in mouse bone marrow cells. These breaks were also present in chicken erythrocyte DNA, which is also highly condensed. These breaks were not observed under neutral pH conditions nor under denaturing conditions not involving alkali, suggesting that these sites are alkali-sensitive and do not represent preexisting single-strand breaks. The high frequency of such sites in sperm from healthy mouse and human donors suggests that they represent a functional characteristic of condensed chromatin rather than DNA damage.     

Transgenic modifications of silkworms as a means to obtain therapeutic biomolecules and protein fibers with exceptional properties

Transgenic modification of Bombyx mori silkworms is a benign approach for the production of silk fibers with extraordinary properties and also to generate therapeutic proteins and other biomolecules for various applications. Silk fibers with fluorescence lasting more than a year, natural protein fibers with strength and toughness exceeding that of spider silk, proteins and therapeutic biomolecules with exceptional properties have been developed using transgenic technology. The transgenic modifications have been done primarily by modifying the silk sericin and fibroin genes and also the silk producing glands. Although the genetic modifications were typically performed using the sericin 1 and other genes, newer techniques such as CRISPR/Cas9 have enabled successful modifications of both the fibroin H-chain and L-chain. Such modifications have led to the production of therapeutic proteins and other biomolecules in reasonable quantities at affordable costs for tissue engineering and other medical applications. Transgenically modified silkworms also have distinct and long-lasting fluorescence useful for bioimaging applications. This review presents an overview of the transgenic techniques for modifications of B. mori silkworms and the properties obtained due to such modifications with particular focus on production of growth factors, fluorescent proteins, and high performance protein fibers.     

The Curation of Genetic Variants: Difficulties and Possible Solutions

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods.     

Proteasome and p97 mediate mitophagy and degradation of mitofusins induced by Parkin

Damage to mitochondria can lead to the depolarization of the inner mitochondrial membrane, thereby sensitizing impaired mitochondria for selective elimination by autophagy. However, fusion of uncoupled mitochondria with polarized mitochondria can compensate for damage, reverse membrane depolarization, and obviate mitophagy. Parkin, an E3 ubiquitin ligase that is mutated in monogenic forms of Parkinson's disease, was recently found to induce selective autophagy of damaged mitochondria. Here we show that ubiquitination of mitofusins Mfn1 and Mfn2, large GTPases that mediate mitochondrial fusion, is induced by Parkin upon membrane depolarization and leads to their degradation in a proteasome- and p97-dependent manner. p97, a AAA+ ATPase, accumulates on mitochondria upon uncoupling of Parkin-expressing cells, and both p97 and proteasome activity are required for Parkin-mediated mitophagy. After mitochondrial fission upon depolarization, Parkin prevents or delays refusion of mitochondria, likely by the elimination of mitofusins. Inhibition of Drp1-mediated mitochondrial fission, the proteasome, or p97 prevents Parkin-induced mitophagy.     

Prediction and Analysis of Canonical EF Hand Loop and Qualitative Estimation of Ca2+ Binding Affinity

The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca²⁺ displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amino acid patterns of canonical EF hand sequences obtained from available crystal structures were used to develop a classifier that distinguishes Ca²⁺-binding loops and non Ca²⁺-binding regions with 100% accuracy. To investigate further, we performed a proteome-wide prediction for E. histolytica, and classified known EF-hand proteins. We compared our results with published methods on the E. histolytica proteome scan, and demonstrated our method to be more specific and accurate for predicting potential canonical Ca²⁺-binding loops. Furthermore, we annotated canonical EF-hand motifs and classified them based on their Ca²⁺-binding affinities using support vector machines. Using a novel method generated from position-specific scoring metrics and then tested against three different experimentally derived EF-hand-motif datasets, predictions of Ca²⁺-binding affinities were between 87 and 90% accurate. Our results show that the tool described here is capable of predicting Ca²⁺-binding affinity constants of EF-hand proteins. The web server is freely available at http://202.41.10.46/calb/index.html.     

First evidence of ethylene production by Fusarium mangiferae associated with mango malformation

Malformation is arguably the most crucial disease of mango (Mangifera indica L.) at present. It is receiving great attention not only because of its widespread and destructive nature but also because of its etiology and control is not absolutely understood. Recently, Fusarium mangiferae is found to be associated with mango malformation disease. There are indications that stress ethylene production could be involved in the disease. Here we have shown the first direct evidence of production of ethylene in pure culture of F. mangiferae obtained from mango. The study also revealed that all the isolates dissected from mango acquire morphological features of F. mangiferae showing most similarity to the features of species with accepted standard features. The isolates of F. mangiferae from mango were observed to produce ethylene in significant amounts, ranging from 9.28–13.66 n mol/g dry wt/day. The findings presented here suggest that F. mangiferae could contribute to the malformation of mango by producing ethylene and probably stimulating stress ethylene production in malformed tissue of mango. Ethylene might be produced through 2-oxoglutarate-dependent oxygenase-type ethylene-forming-enzyme (EFE) pathway in Fusarium sp, which needs to be investigated.     

Skeletal muscle mitochondrial FAT/CD36 content and palmitate oxidation are not decreased in obese women

A reduction in fatty acid oxidation has been associated with lipid accumulation and insulin resistance in the skeletal muscle of obese individuals. We examined whether this decrease in fatty acid oxidation was attributable to a reduction in muscle mitochondrial content and/or a dysfunction in fatty acid oxidation within mitochondria obtained from skeletal muscle of age-matched, lean [body mass index (BMI) = 23.3 +/- 0.7 kg/m2] and obese women (BMI = 37.6 +/- 2.2 kg/m2). The mitochondrial marker enzymes citrate synthase (-34%), beta-hydroxyacyl-CoA dehydrogenase (-17%), and cytochrome c oxidase (-32%) were reduced (P < 0.05) in obese participants, indicating that mitochondrial content was diminished. Obesity did not alter the ability of isolated mitochondria to oxidize palmitate; however, fatty acid oxidation was reduced at the whole muscle level by 28% (P < 0.05) in the obese. Mitochondrial fatty acid translocase (FAT/CD36) did not differ in lean and obese individuals, but mitochondrial FAT/CD36 was correlated with mitochondrial fatty acid oxidation (r = 0.67, P < 0.05). We conclude that the reduction in fatty acid oxidation in obese individuals is attributable to a decrease in mitochondrial content, not to an intrinsic defect in the mitochondria obtained from skeletal muscle of obese individuals. In addition, it appears that mitochondrial FAT/CD36 may be involved in regulating fatty acid oxidation in human skeletal muscle.     

Lysis of mycelium ofFusarium oxysporum f. sp.udum in soil amended with organic matters

Summary Autoclaved or natural field soil amended with 0.1 to 5.0 per cent (W/W) of margosa cake, rice husk and sawdust with or without supplemental nitrogen were tested for lytic activity and bacterial numbers. Generally, non-amended autoclaved soil caused little or no lysis of mycelium ofF. oxysporum f. sp.udum; non-amended natural soil caused more lysis. Amendment of soil with margosa cake, rice husk or saw-dust with or without supplemental nitrogen greatly enhanced its lytic effect on the fungus. The degree of lysis depended on the dosage of amendment used and the stage of its decomposition in the soil. The extent of lysis increased as the bacterial population increased. Amongst bacteria,Bacillus subtilis was very common in most lytic zones.