Partitioning protein structures into domains: why is it so difficult?

This analysis takes an in-depth look into the difficulties encountered by automatic methods for domain decomposition from three-dimensional structure. The analysis involves a multi-faceted set of criteria including the integrity of secondary structure elements, the tendency toward fragmentation of domains, domain boundary consistency and topology. The strength of the analysis comes from the use of a new comprehensive benchmark dataset, which is based on consensus among experts (CATH, SCOP and AUTHORS of the 3D structures) and covers 30 distinct architectures and 211 distinct topologies as defined by CATH. Furthermore, over 66% of the structures are multi-domain proteins; each domain combination occurring once per dataset. The performance of four automatic domain assignment methods, DomainParser, NCBI, PDP and PUU, is carefully analyzed using this broad spectrum of topology combinations and knowledge of rules and assumptions built into each algorithm. We conclude that it is practically impossible for an automatic method to achieve the level of performance of human experts. However, we propose specific improvements to automatic methods as well as broadening the concept of a structural domain. Such work is prerequisite for establishing improved approaches to domain recognition. (The benchmark dataset is available from http://pdomains.sdsc.edu).     

Why is it getting more difficult to successfully artificially inseminate dairy cows?

Successfully using artificial insemination (AI) is defined as getting cows pregnant when the farmer wants them in-calf and making the best use of appropriate genetic potential. Over the past 30 to 50 years, the percentage of animals in oestrus that stand-to-be-mounted (STBM) has declined from 80% to 50%, and the duration of STBM from 15 h to 5 h; both in parallel with a reduction in first-service-pregnancy-rate from 70% to 40%. Meanwhile, the incidence of lameness and mastitis has not decreased; and it takes more than an extra 40 and 18 days, respectively, to get a lame or mastitic cow in-calf compared to healthy herd-mates. The intensity of oestrus is 50% lower in severely lame cows, and fewer lame cows ovulate. Luteal phase milk progesterone concentrations are also 50% lower in lame cows, and follicular phase oestradiol is also lower in non-ovulating lame cows compared to ovulating animals. Furthermore, lame cows that do not ovulate do not have an LH surge, and the LH pulse frequency in their late follicular phase is lower (0.53 v. 0.76 pulses/h). Thus, we suggest that the stress of lameness reduces LH pulsatility required to drive oestradiol production by the dominant follicle. The consequent low oestradiol results in less-intense oestrus behaviour and failure to initiate an LH surge; hence there is no ovulation. A series of experimental studies substantiate our hypothesis that events activating the hypothalamus–pituitary–adrenal axis interfere at both the hypothalamus and the pituitary level to disrupt LH and oestradiol secretion, and thus the expression of oestrus behaviour. Our inability to keep stress at a minimum by appropriately feeding and housing high-production cows is leading to a failure to meet genetic potential for yield and fertility. We must provide realistic solutions soon, if we want to successfully use AI to maintain a sustainable dairy industry for the future.     

Opinion: peroxisomal-protein import: is it really that complex?

Peroxisomal enzymes are synthesized in the cytoplasm and imported post-translationally across the peroxisome membrane. Unlike other organelles with a sealed membrane, peroxisomes can import folded enzymes, and they seem to lack intraperoxisomal chaperones. Here, we propose a mechanistic model for the early steps in peroxisomal-matrix-enzyme import, which might help to explain the unusual features of this process.     

Where is the right path heading from the centromere to spindle microtubules?

The kinetochore is a large protein complex that ensures accurate chromosome segregation during mitosis by connecting the centromere and spindle microtubules. One of the kinetochore sub-complexes, the constitutive centromere-associated network (CCAN), associates with the centromere and recruits another sub-complex, the KMN (KNL1, Mis12, and Ndc80 complexes) network (KMN), which binds to spindle microtubules. The CCAN-KMN interaction is mediated by two parallel pathways (CENP-C- and CENP-T-pathways) in the kinetochore, which bridge the centromere and microtubules. Here, we discuss dynamic protein-interaction changes in the two pathways that couple the centromere with spindle microtubules during mitotic progression.     

How is it that microsatellites and random oligonucleotides uncover DNA fingerprint patterns?

Minisatellites, microsatellites, and short random oligonucleotides all uncover highly polymorphic DNA fingerprint patterns in Southern analysis of genomic DNA that has been digested with a restriction enzyme having a 4-bp specificity. The polymorphic nature of the fragments is attributed to tandem repeat number variation of embedded minisatellite sequences. This explains why DNA fingerprint fragments are uncovered by minisatellite probes, but does not explain how it is that they are also uncovered by microsatellite and random oligonucleotide probes. To clarify this phenomenon, we sequenced a large bovine genomic BamHI restriction fragment hybridizing to the Jeffreys 33.6 minisatellite probe and consisting of small and large Sau3A-resistant subfragments. The large Sau3A subfragment was found to have a complex architecture, consisting of two different minisatellites, flanked and separated by stretches of unique DNA. The three unique sequences were characterized by sequence simplicity, that is, a higher than chance occurrence of tandem or dispersed repetition of simple sequence motifs. This complex repetitive structure explains the absence of Sau3A restriction sites in the large Sau3A subfragment, yet provides this subfragment with the ability to hybridize to a variety of probe sequences. It is proposed that a large class of interspered tracts sharing this complex yet simplified sequence structure is found in the genome. Each such tract would have a broad ability to hybridize to a variety of probes, yet would exhibit a dearth of restriction sites. For each restriction enzyme having 4-bp specificity, a subclass of such tracts, completely lacking the corresponding restriction sites, will be present. On digestion with the given restriction enzyme, each such tract would form a large fragment. The largest fragments would be those that contained one or more long minisatellite tracts. Some of these large fragments would be highly polymorphic by virtue of the included minisatellite sequences; by virtue of their complex structure, all would be capable of hybridizing to a wide variety of probes, uncovering a DNA fingerprint pattern.     

Interaction between valence of empathy and familiarity: is it difficult to empathize with the positive events of a stranger?

Background

Empathy in humans is thought to have evolved via social interactions caused by the formation of social groups. Considering the role of empathy within a social group, there might be a difference between emotional empathy for strangers and familiar others belonging to the same social group. In this study, we used the global field power (GFP) index to investigate empathic brain activity during observation of a cue indicating either a negative or positive image viewed by a stranger or close friend.

Methods

Sixteen healthy participants observed a partner performing an emotional gambling task displayed on a monitor. After the partner''s choice-response, a frowning or smiling face symbol was simultaneously presented to the participant’s monitor while a negative or positive emotional image was presented to the partner’s monitor. All participants observed a control condition (CT) showing a computer trial, a stranger-observation condition (SO) showing the trial of a stranger, and a friend-observation condition (FO) to observe the trial of a close friend. During these observations, participants’ event-related potentials (ERPs) were recorded to calculate GFP, and after the task, a subjective assessment of their feelings was measured.

Results

Positive emotion was significantly larger under the FO compared to the CT and the SO. Significantly larger negative emotion was found under the SO and FO compared to the CT. In response to a positive cue, significantly larger GFP during 300 to 600 ms was observed under the FO compared to the CT and SO. In response to a negative cue, significantly larger GFP was observed under the FO and SO compared to the CT. A significantly larger GFP under the SO was found in response to only a negative cue. Topographic map analysis suggested that these differences were related to frontal-occipital dynamics. GFP was significantly correlated with empathic trait.

Conclusion

These results revealed that familiarity with another person has different effects depending on the valence of empathy. Negative empathy, including the danger perception function, might easily occur even among strangers, whereas positive empathy related to nursing and supporting an inner group does not happen easily with strangers.     

TonB or not TonB: is that the question?

Bacteria are able to survive in low-iron environments by sequestering this metal ion from iron-containing proteins and other biomolecules such as transferrin, lactoferrin, heme, hemoglobin, or other heme-containing proteins. In addition, many bacteria secrete specific low molecular weight iron chelators termed siderophores. These iron sources are transported into the Gram-negative bacterial cell through an outer membrane receptor, a periplasmic binding protein (PBP), and an inner membrane ATP-binding cassette (ABC) transporter. In different strains the outer membrane receptors can bind and transport ferric siderophores, heme, or Fe3+ as well as vitamin B12, nickel complexes, and carbohydrates. The energy that is required for the active transport of these substrates through the outer membrane receptor is provided by the TonB/ExbB/ExbD complex, which is located in the cytoplasmic membrane. In this minireview, we will briefly examine the three-dimensional structure of TonB and the current models for the mechanism of TonB-dependent energy transduction. Additionally, the role of TonB in colicin transport will be discussed.     

Race,ethnicity and disciplinary divides: what is the path forward?

We pose several questions that emerged for us from Valdez and Golash-Boza’s “U.S. Racial and Ethnic Relations in the twenty-first Century.” First, we raise questions about their framing of the problem with current scholarship – are immigration/ethnicity and race scholars talking past each other or are they having more fundamental disagreements? Second, we raise questions about their critique of the “the race literature” – do too many of us ignore questions of agency and inclusion? Finally, we raise questions about the stability and utility of the concepts they deploy (“race” and “ethnicity”) and draw on recent scholarship that has argued that we need new language or frameworks to adequately describe the reality on the ground.     

Why is it so difficult to construct Q(i) site mutants in Chlamydomonas reinhardtii?

The cytochrome b(6)f complex catalyses electron transfer from plastoquinol to a hydrosoluble acceptor (plastocyanin), while building up an electrochemical proton gradient. Oxidation and reduction of plastoquinol occur respectively at the Q(o) site (exposed on the luminal side of the thylakoid membrane) and at the Q(i) site (facing the stroma). The discovery of an additional c'-type heme in the Q(i) site has cast a new light on the difficulties previously encountered to obtain mutants at this site. In this work, we critically examine our unsuccessful attempts to obtain Q(i) site mutants based on sequence and structure homology between cytochrome b(6)f and bc(1) complexes.     

What the papers say: Where is the somatic mutation that causes aging?

It has been proposed that somatic mutations make major contributions to aging. The first paper, based on a gene knock-in mouse, supports a contributory role for mutation in mtDNA in aging, but does not support a damaged-mtDNA-producing-more-damaged-mtDNA hypothesis. The second paper indicates some GC-rich sequences in the nuclear DNA are more sensitive to oxidative damage than mtDNA. As a result, key genes involved in brain function and mitochondrial function are progressively inactivated with age. Failure in these nucleus-encoded mitochondrial genes may be a primary reason for mitochondrial failure in old age.