An automated image-based workflow for detecting megabenthic fauna in optical images with examples from the Clarion-Clipperton Zone

Recent advances in optical underwater imaging technologies enable the acquisition of huge numbers of high-resolution seafloor images during scientific expeditions. While these images contain valuable information for non-invasive monitoring of megabenthic fauna, flora and the marine ecosystem, traditional labor-intensive manual approaches for analyzing them are neither feasible nor scalable. Therefore, machine learning has been proposed as a solution, but training the respective models still requires substantial manual annotation. Here, we present an automated image-based workflow for Megabenthic Fauna Detection with Faster R-CNN (FaunD-Fast). The workflow significantly reduces the required annotation effort by automating the detection of anomalous superpixels, which are regions in underwater images that have unusual properties relative to the background seafloor. The bounding box coordinates of the detected anomalous superpixels are proposed as a set of weak annotations, which are then assigned semantic morphotype labels and used to train a Faster R-CNN object detection model. We applied this workflow to example underwater images recorded during cruise SO268 to the German and Belgian contract areas for Manganese-nodule exploration, within the Clarion-Clipperton Zone (CCZ). A performance assessment of our FaunD-Fast model showed a mean average precision of 78.1% at an intersection-over-union threshold of 0.5, which is on a par with competing models that use costly-to-acquire annotations. In more detail, the analysis of the megafauna detection results revealed that ophiuroids and xenophyophores were among the most abundant morphotypes, accounting for 62% of all the detections within the surveyed area. Investigating the regional differences between the two contract areas further revealed that both megafaunal abundance and diversity was higher in the shallower German area, which might be explainable by the higher food availability in form of sinking organic material that decreases from east-to-west across the CCZ. Since these findings are consistent with studies based on conventional image-based methods, we conclude that our automated workflow significantly reduces the required human effort, while still providing accurate estimates of megafaunal abundance and their spatial distribution. The workflow is thus useful for a quick but objective generation of baseline information to enable monitoring of remote benthic ecosystems.

Peroxide sensors for the fission yeast stress-activated mitogen-activated protein kinase pathway

The Schizosaccharomyces pombe stress-activated Sty1p/Spc1p mitogen-activated protein (MAP) kinase regulates gene expression through the Atf1p and Pap1p transcription factors, homologs of human ATF2 and c-Jun, respectively. Mcs4p, a response regulator protein, acts upstream of Sty1p by binding the Wak1p/Wis4p MAP kinase kinase kinase. We show that phosphorylation of Mcs4p on a conserved aspartic acid residue is required for activation of Sty1p only in response to peroxide stress. Mcs4p acts in a conserved phospho-relay system initiated by two PAS/PAC domain-containing histidine kinases, Mak2p and Mak3p. In the absence of Mak2p or Mak3p, Sty1p fails to phosphorylate the Atf1p transcription factor or induce Atf1p-dependent gene expression. As a consequence, cells lacking Mak2p and Mak3p are sensitive to peroxide attack in the absence of Prr1p, a distinct response regulator protein that functions in association with Pap1p. The Mak1p histidine kinase, which also contains PAS/PAC repeats, does not regulate Sty1p or Atf1p but is partially required for Pap1p- and Prr1p-dependent transcription. We conclude that the transcriptional response to free radical attack is initiated by at least two distinct phospho-relay pathways in fission yeast.

Sin1: an evolutionarily conserved component of the eukaryotic SAPK pathway

The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. We have identified a protein, Sin1, that interacts with Sty1/Spc1 which is a member of a new evolutionarily conserved gene family. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent. Importantly, Sin1 is not required for activation of Sty1/Spc1 but is required for stress-dependent transcription via its substrate, Atf1. We find that in the absence of Sin1, Sty1/Spc1 appears to translocate to the nucleus but Atf1 is not fully phosphorylated and becomes unstable in response to environmental stress. Sin1 is also required for effective transcription via the AP-1 factor Pap1 but does not prevent its nuclear translocation. Remarkably chimaeric fusions of sin1 with chicken sin1 sequences rescue loss of sin1 function. We conclude that Sin1 is a novel component of the eukaryotic SAPK pathway.

The Mcs4 response regulator coordinately controls the stress-activated Wak1-Wis1-Sty1 MAP kinase pathway and fission yeast cell cycle

The fission yeast Sty1 MAP kinase is required for cell cycle control, initiation of sexual differentiation, and protection against cellular stress. Like the mammalian JNK/SAPK and p38/CSBP1 MAP kinases, Sty1 is activated by a range of environmental insults including osmotic stress, hydrogen peroxide, menadione, heat shock, and the protein synthesis inhibitor anisomycin. We have identified an upstream regulator that mediates activation of the Sty1 MAP kinase by multiple environmental stresses as the product of the mitotic catastrophe suppressor, mcs4. Mcs4 is structurally and functionally homologous to the budding yeast SSK1 response regulator, suggesting that the eukaryotic stress-activated MAP kinase pathway is controlled by a conserved two-component system. Mcs4 acts upstream of Wak1, a homolog of the SSK2 and SSK22 MEK kinases, which transmits the stress signal to the Wis1 MEK. We show that the Wis1 MEK is controlled by an additional pathway that is independent of both Mcs4 and the Wak1 MEK kinase. Furthermore, we demonstrate that Mcs4 is required for the correct timing of mitotic initiation by mechanisms both dependent and independent on Sty1, indicating that Mcs4 coordinately controls cell cycle progression with the cellular response to environmental stress.

Identification of a cdk-activating kinase in fission yeast

We have identified a second cyclin-dependent kinase (cdk) in fission yeast, crk1, which encodes a 335 amino acid protein that is most closely related to the KIN28 gene product from Saccharomyces cerevisiae and to a cdk activating kinase (CAK) encoded by the MO15 gene from Xenopus laevis, crk1 is essential for viability and delta crk1 cells arrest with septa and condensed chromatin. We show that Crk1 associates with the Mcs2 mitotic catastrophe suppressor, a cyclin H-like molecule, and overexpression of crk1 rescues the cell-cycle arrest defect of a mcs2-75 cdc2-3w cdc25-22 triple mutant at high temperature. The Crk1-Mcs2 complex possesses CAK activity in vitro in that it phosphorylates human Cdk2 on Thr160 which results in its activation in the presence of cyclin A. In addition Crk1-Mcs2 effectively phosphorylates a peptide corresponding to the C-terminal repeat domain (CTD) of RNA polymerase II. We demonstrate that crk1 is allelic to the mcs6 mitotic catastrophe suppressor and that the X.laevis MO15 gene rescues the cell-cycle arrest of an mcs6-13 cdc2-3w cdc25-22 at high temperature. Together these data suggest that the Crk1-Mcs2 complex is a CAK that interacts genetically with Cdc2 in fission yeast.

Pyp1 and Pyp2 PTPases dephosphorylate an osmosensing MAP kinase controlling cell size at division in fission yeast

Simultaneous inactivation of pyp1 and pyp2 PTPases in fission yeast leads to aberrant cell morphology and growth arrest. Spontaneous recessive mutations that bypass the requirement for pyp1 and pyp2 and reside in two complementation groups were isolated, sty1 and sty2. sty1- and sty2- mutant cells are substantially delayed in the timing of mitotic initiation. We have isolated the sty1 gene, which encodes a MAP kinase that is closely related to a subfamily of MAP kinases regulated by osmotic stress including Saccharomyces cervisiae HOG1 and human CSBP1. We find that sty2 is allelic to the wis1 MAP kinase kinase and that delta sty1 and delta wis1 cells are unable to grow in high osmolarity medium. Osmotic stress induces both tyrosine phosphorylation of Sty1 and a reduction in cell size at division. Pyp2 associates with and tyrosine dephosphorylates Sty1 in vitro. We find that wis1-dependent induction of pyp2 mRNA is responsible for tyrosine dephosphorylation of Sty1 in vivo on prolonged exposure to osmotic stress. We conclude that Pyp1 and Pyp2 are tyrosine-specific MAP kinase phosphatases that inactivate an osmoregulated MAP kinase, Sty1, which acts downstream of the Wis1 MAP kinase kinase to control cell size at division in fission yeast.

Molecular and functional characterisation of E2F-5, a new member of the E2F family

The transcription factor DRTF1/E2F is implicated in the control of cellular proliferation due to its interaction with key regulators of cell cycle progression, such as the retinoblastoma tumour suppressor gene product and related pocket proteins, cyclins and cyclin-dependent kinases. DRTF1/E2F DNA binding activity arises when a member of two distinct families of proteins, DP and E2F, interact as DP/E2F heterodimers. Here, we report the isolation and characterisation of a new member of the E2F family of proteins, called E2F-5. E2F-5 was isolated through a yeast two hybrid assay in which a 14.5 d.p.c. mouse embryo library was screened for molecules capable of binding to murine DP-1, but also interacts with all known members of the DP family of proteins. E2F-5 exists as a physiological heterodimer with DP-1 in the generic DRTF1/E2F DNA binding activity present in mammalian cell extracts, an interaction which results in co-operative DNA binding activity and transcriptional activation through the E2F site. A potent transcriptional activation domain, which functions in both yeast and mammalian cells and resides in the C-terminal region of E2F-5, is specifically inactivated upon pocket protein binding. Comparison of the sequence with other members of the family indicates that E2F-5 shows a greater level of similarity with E2F-4 than to E2F-1, -2 and -3. The structural and functional similarity of E2F-5 and E2F-4 defines a subfamily of E2F proteins.

[Postlaparoscopic pain syndrome. Results of a prospective, randomized study]

The so-called post-laparoscopic algesia is a specific impairment of about 63% of the patients who undergo laparoscopic surgical operations. This impairment takes the form of mild to moderate shoulder pain. Eliminating the causes of pain has a clear advantage over symptomatic treatment using analgetics, a fact worth a good consideration especially with the post-operative sojourn at the hospital becoming shorter and shorter. In a prospective controlled study, involving 42 patients subdivided into four groups namely, higher or lower insufflation pressures, chemically inert insufflation gas and control groups; the use of analgetics, lung function, operation duration, amount of insufflated gas, intraperitoneal pH-values and post-operative complications in the various subgroups were compared to each other with regard to post-operative pain perception. The results did not show any significant differences among the groups regarding the main parameters like pH-value or different insufflation pressures etc. These results led to the termination of the study based on the raised criteria since we anticipated the actual cause of the shoulder pain to be due to an unknown factor. By the evaluation of the individual data, it became apparent that, the pains increase with increasing gas consumption, a fact which led to assumption that the pains are caused by a physical effect such as the cooling of the peritoneum.

CDC7 protein kinase activity is required for mitosis and meiosis in Saccharomyces cerevisiae

The product of the CDC7 gene of Saccharomyces cerevisiae has multiple cellular functions, being needed for the initiation of DNA synthesis during mitosis as well as for synaptonemal complex formation and commitment to recombination during meiosis. The CDC7 protein has protein kinase activity and contains the conserved residues characteristic of the protein kinase catalytic domain. To determine which of the cellular functions of CDC7 require this protein kinase activity, we have mutated some of the conserved residues within the CDC7 catalytic domain and have examined the ability of the mutant proteins to support mitosis and meiosis. The results indicate that the protein kinase activity of the CDC7 gene product is essential for its function in both mitosis and meiosis and that this activity is potentially regulated by phosphorylation of the CDC7 protein.

Characterisation of the CDC7 gene product of Saccharomyces cerevisiae as a protein kinase needed for the initiation of mitotic DNA synthesis

The product of the CDC7 gene of Saccharomyces cerevisiae, which is needed for the initiation of mitotic DNA synthesis, has homology with known and putative protein kinases. This homology is confined to the kinase catalytic domain, which has a unique organisation in CDC7. To demonstrate that, nonetheless, CDC7 protein has kinase activity, the gene was subcloned under the control of the SP6 promoter. Protein synthesised by transcription and translation in vitro was capable of transferring 32P from [gamma-32P]ATP to histone. This activity was not dependent on Ca2+ or cyclic nucleotides. A mutation of CDC7 constructed in vitro, in which the organisation of the kinase catalytic domain was converted to that found in all other similar enzymes, was unable to function in vivo, as judged by its inability to complement the cdc7-1 allele. This suggests that the abnormal structure of the CDC7 catalytic domain is a key element in the cellular function of this protein in initiating DNA synthesis.

Dynamic auditory localization: systematic replication of the auditory velocity function

Two experiments explored the capability of normal-hearing adults to judge the apparent velocity of an unseen moving sound source. In exper. I, 9 naive and, 1 experienced S judged the velocity of a moving source emitting a .5-kc/s tone at 50 db SPL. S's head was in the center of a circle of 1.88-m radius swept by a small loudspeaker. In exper. II the sound was a low-pass-filtered (0.1-1 kc/s) noise at 50 db sound spectrum level. In both experiments perceived velocity was directly proportional to the actual velocity of the source. These results support out initial observations (Waugh et al, J. Aud. Res., 1979, 19, 103-1 10) that auditory velocity discrimination can be described as a power function with an exponent of 1.0. In exper. II the Ss also varied the sound source velocity by means of a variable resistor to produce a perceived velocity of 100 degrees/sec. Performance on the adaptive velocity production task was successfully predicted from the data of the absolute velocity judgment task. The Weber fraction was .052 for relatively fast-moving sound sources (100 degrees/sec). The ability to discriminate sound source velocity appears to be a well-defined feature of the dynamic binaural spatial system.