Molecular basis of cross‐species ACE2 interactions with SARS‐CoV‐2‐like viruses of pangolin origin

Correction to: The EMBO Journal (2021) 40: e107786. DOI 10.15252/embj.2021107786 | Published online 8 June 2021The authors would like to add three references to the paper: Starr et al and Zahradník et al also reported that the Q498H or Q498R mutation has enhanced binding affinity to ACE2; and Liu et al reported on the binding of bat coronavirus to ACE2.Starr et al and Zahradník et al have now been cited in the Discussion section, and the following sentence has been corrected from:“According to our data, the SARS‐CoV‐2 RBD with Q498H increases the binding strength to hACE2 by 5‐fold, suggesting the Q498H mutant is more ready to interact with human receptor than the wildtype and highlighting the necessity for more strict control of virus and virus‐infected animals”.to“Here, according to our data and two recently published papers, the SARS‐CoV‐2 RBD with Q498H or Q498R increases the binding strength to hACE2 (Starr et al, 2020; Zahradník et al, 2021), suggesting the mutant with Q498H or Q498R is more ready to interact with human receptor than the wild type and highlighting the necessity for more strict control of virus and virus‐infected animals”.The Liu et al citation has been added to the following sentence:“In another paper published by our group recently, RaTG13 RBD was found to bind to hACE2 with much lower binding affinity than SARS‐CoV‐2 though RaTG13 displays the highest whole‐genome sequence identity (96.2%) with the SARS‐CoV‐2 (Liu et al, 2021)”.Additionally, the authors have added the GISAID accession IDs to the sequence names of the SARS‐CoV‐2 in two human samples (Discussion section). To make identification unambiguous, the sequence names have been updated from “SA‐lsf‐27 and SA‐lsf‐37” to “GISAID accession ID: EPI_ISL_672581 and EPI_ISL_672589”.Lastly, the authors declare in the Materials and Methods section that all experiments employed SARS‐CoV‐2 pseudovirus in cultured cells. These experiments were performed in a BSL‐2‐level laboratory and approved by Science and Technology Conditions Platform Office, Institute of Microbiology, Chinese Academy of Sciences.These changes are herewith incorporated into the paper.     

Gastric stem cells promote inflammation and gland remodeling in response to Helicobacter pylori via Rspo3‐Lgr4 axis

Helicobacter pylori is a pathogen that colonizes the stomach and causes chronic gastritis. Helicobacter pylori can colonize deep inside gastric glands, triggering increased R‐spondin 3 (Rspo3) signaling. This causes an expansion of the “gland base module,” which consists of self‐renewing stem cells and antimicrobial secretory cells and results in gland hyperplasia. The contribution of Rspo3 receptors Lgr4 and Lgr5 is not well explored. Here, we identified that Lgr4 regulates Lgr5 expression and is required for H. pylori‐induced hyperplasia and inflammation, while Lgr5 alone is not. Using conditional knockout mice, we reveal that R‐spondin signaling via Lgr4 drives proliferation of stem cells and also induces NF‐κB activity in the proliferative stem cells. Upon exposure to H. pylori, the Lgr4‐driven NF‐κB activation is responsible for the expansion of the gland base module and simultaneously enables chemokine expression in stem cells, resulting in gland hyperplasia and neutrophil recruitment. This demonstrates a connection between R‐spondin‐Lgr and NF‐κB signaling that links epithelial stem cell behavior and inflammatory responses to gland‐invading H. pylori.     

Homo floresiensis: a cladistic analysis

The announcement of a new species, Homo floresiensis, a primitive hominin that survived until relatively recent times is an enormous challenge to paradigms of human evolution. Until this announcement, the dominant paradigm stipulated that: 1) only more derived hominins had emerged from Africa, and 2) H. sapiens was the only hominin since the demise of Homo erectus and Homo neanderthalensis. Resistance to H. floresiensis has been intense, and debate centers on two sets of competing hypotheses: 1) that it is a primitive hominin, and 2) that it is a modern human, either a pygmoid form or a pathological individual. Despite a range of analytical techniques having been applied to the question, no resolution has been reached. Here, we use cladistic analysis, a tool that has not, until now, been applied to the problem, to establish the phylogenetic position of the species. Our results produce two equally parsimonious phylogenetic trees. The first suggests that H. floresiensis is an early hominin that emerged after Homo rudolfensis (1.86 Ma) but before H. habilis (1.66 Ma, or after 1.9 Ma if the earlier chronology for H. habilis is retained). The second tree indicates H. floresiensis branched after Homo habilis.     

Lazy hazy days

Scientists have warned about the looming climate crisis for decades, but the world has been slow to act. Are we in danger of making a similar mistake, by neglecting the dangers of other climactic catastrophes? Subject Categories: Biotechnology & Synthetic Biology, Economics, Law & Politics, Evolution & Ecology

On one of my trips to Antarctica, I was enjoined to refer not to “global warming” or even to “climate change.” The former implies a uniform and rather benign process, while the second suggests just a transition from one state to another and seems to minimize all the attendant risks to survival. Neither of these terms adequately or accurately describes what is happening to our planet''s climate system as a result of greenhouse gas emissions; not to mention the effects of urbanization, intensive agriculture, deforestation, and other consequences of human population growth. Instead, I was encouraged to use the term “climate disruption,” which embraces the multiplicity of events taking place, some of them still hard to model, that are altering the planetary ecosystem in dramatic ways.With climate disruption now an urgent and undeniable reality, policymakers are finally waking up to the threats that scientists have been warning about for decades. They have accepted the need for action (UNFCCC Conference of the Parties, ²⁰²¹), even if the commitment remains patchy or lukewarm. But to implement all the necessary changes is a massive undertaking, and it is debatable whether we have enough time left. The fault lies mostly with those who resisted change for so long, hoping the problem would just go away, or denying that it was happening at all. The crisis situation that we face today is because the changes needed simply cannot be executed overnight. It will take time for the infrastructure to be put in place, whether for renewable electricity, for the switch to carbon‐neutral fuels, for sustainable agriculture and construction, and for net carbon capture. If the problems worsen, requiring even more drastic action, at least we do have a direction of travel, though we would be starting off from an even more precarious situation.However, given the time that it has taken—and will still take—to turn around the juggernaut of our industrial society, are we in danger of making the same mistakes all over again, by ignoring the risks of the very opposite process happening in our lifetime? The causes of historic climate cooling are still debated, and though we have fairly convincing evidence regarding specific, sudden events, there is no firm consensus on what is behind longer‐term and possibly cyclical changes in the climate.The two best‐documented examples are the catastrophe of 536–540 AD and the effects of the Laki Haze of 1783–1784. The cause of the 536–540 event is still debated, but is widely believed to have been one or more massive volcanic eruptions that created a global atmospheric dust‐cloud, resulting in a temperature drop of up to 2°C with concomitant famines and societal crises (Toohey et al, ²⁰¹⁶; Helama et al, ²⁰¹⁸). The Laki Haze was caused by the massive outpouring of sulfurous fumes from the Laki eruption in Iceland. Its effects on the climate, though just as immediate, were less straightforward. The emissions, combined with other meteorological anomalies, produced a disruption of the jetstream, as well as other localized effects. In northwest Europe, the first half of the summer of 1783 was exceptionally hot, but the following winters were dramatically cold, and the mean temperature across much of the northern hemisphere is estimated to have dropped by around 1.3°C for 2–3 years (Thordarson & Self, ²⁰⁰³). In Iceland itself, as well as much of western and northern Europe, the effects were even more devastating, with widespread crop failures and deaths of both livestock and humans exacerbated by the toxicity of the volcanic gases (Schmidt et al, ²⁰¹¹).Other volcanic events in recorded time have produced major climactic disturbances, such as the 1816 Tambora eruption in Indonesia, which resulted in “the year without a summer,” marked by temperature anomalies of up to 4°C (Fasullo et al, ²⁰¹⁷), again precipitating worldwide famine. The 1883 Krakatoa eruption produced similar disruption, albeit of a lesser magnitude, though the effects are proposed to have been much longer lasting (Gleckler et al, ²⁰⁰⁶).Much more scientifically challenging is the so‐called Little Ice Age in the Middle Ages, approximately from 1250 to 1700 AD, when global temperatures were significantly lower than in the preceding and following centuries. It was marked by particularly frigid and prolonged winters in the northern hemisphere. There is no strong consensus as to its cause(s) or even its exact dates; nor even that it can be considered a global‐scale event rather than a summation of several localized phenomena. A volcanic eruption in 1257 with similar effects to the one of 1816 has been suggested as an initiating event. Disruption of the oceanic circulation system resulting from prolonged anomalies in solar activity is another possible explanation (Lapointe & Bradley, ²⁰²¹). Nevertheless, and despite an average global cooling of < 1°C, the effects on global agriculture, settlement, migration and trade, pandemics such as the Black Death and perhaps even wars and revolutions, were profound.Once or twice in the past century, we have faced devastating wars, tsunamis and pandemics that seemed to come out of the blue and exacted massive tolls on humanity. From the most recent of each of these, there is a growing realization that, although these events are rare and poorly predictable, we can greatly limit the damage if we prepare properly. Devoting a small proportion of our resources over time, we can build the infrastructure and the mechanisms to cope, when these disasters do eventually strike.Without abandoning any of the emergency measures to combat anthropogenic warming, I believe that the risk of climate cooling needs to be addressed in the same way. The infrastructure for burning fossil fuels needs to be mothballed, not destroyed. Carbon capture needs to be implemented in a way that is rapidly reversible, if this should ever be needed. Alternative transportation routes need to be planned and built in case existing ones become impassable due to ice or flooding. Properly insulated buildings are not just a way of saving energy. They are essential for survival in extreme cold, as those of us who live in the Arctic countries are well aware—but many other regions also experience severe winters, for which we should all prepare.Biotechnology needs to be set to work to devise ways of mitigating the effects of sudden climactic events such as the Laki Haze or the Tambora and Krakatoa eruptions, as well as longer‐term phenomena like the Little Ice Age. Could bacteria be used, for example, to detoxify and dissipate a sulfuric aerosol such as the one generated by the Laki eruption? Methane is generally regarded as a major contributor to the greenhouse effect, but it is short‐lived in the atmosphere. So, could methanogens somehow be harnessed to bring about a temporary rise in global temperatures to offset short‐term cooling effects of a volcanic dust‐cloud?We already have a global seed bank in Svalbard (Asdal & Guarino, ²⁰¹⁸): It might easily be expanded to include a greater representation of cold‐resistant varieties of the world''s crop plants that might one day be vital to human survival. And, the experience of the Laki Haze indicates a need for varieties capable of withstanding acid rains and other volcanic pollutants, as well as drought and water saturation. An equivalent (embryo) bank for strains of agriculturally important animals potentially threatened by the effects of abrupt cooling of the climate or catastrophic toxification of the atmosphere is also worth considering.It has generally been thought impractical and pointless to prepare for even rarer events, such as cometary impacts, but events that have occurred repeatedly in recorded history and over an even longer time scale (Helama et al, ²⁰²¹) are likely to happen again. We should and can be better prepared. This is not to say that we should pay attention to every conspiracy theorist or crank, or paid advocates for energy corporations that seek short‐term profits at the expense of long‐term survival, but the dangers of climate disruption of all kinds are too great to ignore. Instead of our current rather one‐dimensional thinking, we need an “all‐risks” approach to the subject: learning from the past and the present to prepare for the future.     

Small-bodied humans from Palau, Micronesia

Newly discovered fossil assemblages of small bodied Homo sapiens from Palau, Micronesia possess characters thought to be taxonomically primitive for the genus Homo.

Background

Recent surface collection and test excavation in limestone caves in the rock islands of Palau, Micronesia, has produced a sizeable sample of human skeletal remains dating roughly between 940-2890 cal ybp.

Principle Findings

Preliminary analysis indicates that this material is important for two reasons. First, individuals from the older time horizons are small in body size even relative to “pygmoid” populations from Southeast Asia and Indonesia, and thus may represent a marked case of human insular dwarfism. Second, while possessing a number of derived features that align them with Homo sapiens, the human remains from Palau also exhibit several skeletal traits that are considered to be primitive for the genus Homo.

Significance

These features may be previously unrecognized developmental correlates of small body size and, if so, they may have important implications for interpreting the taxonomic affinities of fossil specimens of Homo.     

Like Father,Like Son: Assessment of the Morphological Affinities of A.L. 288–1 (A. afarensis), Sts 7 (A. africanus) and Omo 119–73–2718 (Australopithecus sp.) through a Three-Dimensional Shape Analysis of the Shoulder Joint

The postcranial evidence for the Australopithecus genus indicates that australopiths were able bipeds; however, the morphology of the forelimbs and particularly that of the shoulder girdle suggests that they were partially adapted to an arboreal lifestyle. The nature of such arboreal adaptations is still unclear, as are the kind of arboreal behaviors in which australopiths might have engaged. In this study we analyzed the shape of the shoulder joint (proximal humerus and glenoid cavity of the scapula) of three australopith specimens: A.L. 288–1 (A. afarensis), Sts 7 (A. africanus) and Omo 119–73–2718 (Australopithecus sp.) with three-dimensional geometric morphometrics. The morphology of the specimens was compared with that of a wide array of living anthropoid taxa and some additional fossil hominins (the Homo erectus specimen KNM-WT 15000 and the H. neanderthalensis specimen Tabun 1). Our results indicate that A.L. 288–1 shows mosaic traits resembling H. sapiens and Pongo, whereas the Sts 7 shoulder is most similar to the arboreal apes and does not present affinities with H. sapiens. Omo 119–73–2718 exhibits morphological affinities with the more arboreal and partially suspensory New World monkey Lagothrix. The shoulder of the australopith specimens thus shows a combination of primitive and derived traits (humeral globularity, enhancement of internal and external rotation of the joint), related to use of the arm in overhead positions. The genus Homo specimens show overall affinities with H. sapiens at the shoulder, indicating full correspondence of these hominin shoulders with the modern human morphotype.     

Comet assay for quantification of the increased DNA damage burden in primary human chondrocytes with aging and osteoarthritis

It is known that chondrocytes from joints with osteoarthritis (OA) exhibit high levels of DNA damage, but the degree to which chondrocytes accumulate DNA damage during “normal aging” has not been established. The goal of this study was to quantify the DNA damage present in chondrocytes obtained from cadaveric donors of a wide age range, and to compare the extent of this damage to OA chondrocytes. The alkaline comet assay was used to measure the DNA damage in normal cartilage from the ankle (talus) and the knee (femur) of cadaveric donors, as well as in OA chondrocytes obtained at the time of total knee replacement. Chondrocytes from younger donors (<45 years) had less DNA damage than older donors (>70 years) as assessed by the percentage of DNA in the comet “tail”. In donors between 50 and 60 years old, there was increased DNA damage in chondrocytes from OA cartilage as compared to cadaveric. Talar chondrocytes from 23 donors between the ages of 34 and 78 revealed a linear increase in DNA damage with age (R ² = 0.865, p < 0.0001). A “two‐tailed” comet assay was used to demonstrate that most of the accumulated damage is in the form of strand breaks as opposed to alkali‐labile base damage. Chondrocytes from young donors required 10 Gy irradiation to recapitulate the DNA damage present in chondrocytes from older donors. Given the potential for DNA damage to contribute to chondrocyte dysfunction and senescence, this study supports the investigation of mechanisms by which hypo‐replicative cell types accumulate high levels of damage.     

Standing on the shoulders of microbes: How cancer biologists are expanding their view of hard‐to‐kill persister cells

Similar to persister bacterial cells that survive antibiotic treatments, some cancer cells can evade drug treatments. This Commentary discusses the different classes of persister cells and their implications for developing more efficient cancer treatments. Subject Categories: Cancer

Similar to persister bacterial cells that survive antibiotic treatments, small populations of cancer cells can evade drug treatments and cause recurrent disease. This Commentary discusses the different classes of persister cells and their implications for developing more efficient cancer treatments.In 1944, Joseph Bigger, a lieutenant‐colonel in the British Royal Army Medical Corps, reported a peculiar population of bacteria that could survive very high concentrations of penicillin (Bigger, 1944). He termed these hard‐to‐kill cells “persisters” and argued they might explain the limited success of penicillin in curing infections. At the time, 16 years after antibiotics revolutionized bacterial infection treatment, this was a groundbreaking hypothesis as it was largely believed that partial killing was mostly due to inadequate blood supply or tissue barriers. Later on, the understanding that cell‐intrinsic properties may contribute to transient drug tolerance sparked research aimed at targeting microbial persister cells. In a seminal paper, Sherma and colleagues (Sharma et al, 2010) showed that reversible cell‐intrinsic resistance can also be observed in cancer cells in response to therapy. Similar to bacterial persisters, these cancer persister cells gave rise to a drug‐sensitive cell progeny following a short “drug‐holiday” and did not harbor any known resistance‐mediating alteration mutation. However, in contrast to microbial persisters that are largely dormant, a small fraction of cancer persister cells were able to resume proliferation even under continued drug treatment. Understanding the similarities and differences between cancer and microbial persister cells is pivotal to devise approaches to eliminate them (Fig 1).Open in a separate windowFigure 1Different persister classes(A) Classic persisters, (B) targeted‐persisters, and (C) immune‐persisters. The mechanism of escape is dependent on the mode of action of the drug. While classical persisters are common to both bacteria and cancer cells, other persister classes are cancer‐specific and are associated with the ability of cancer cells to probe a wide range of cells states and lineage trajectories.So why can some bacteria persist in the face of therapy? The answer largely lays in the mode of action of antimicrobial drugs. Penicillin and newer generation antibiotics target bacterial cell division. As such, if the bacteria are dormant or reside in a low metabolic state, they are unafflicted by the drug. Dormant bacteria are frequently resistant to multiple stressors and drugs making them difficult to eradicate even with a very aggressive treatment. Unsurprisingly, similar phenomena are observed in the context of chemotherapy treatments in cancer. Like antibiotics, early cancer therapies were largely based on drugs that target highly proliferative cells. Sustained proliferation in the absence of external stimuli is one of the hallmarks of cancer. Because cancer cells divide more frequently than most normal cells, they are more likely to be killed by chemotherapy treatment. As both antibiotics and chemotherapy treatments target proliferating cells, it is not surprising that cell dormancy was linked to cell persistence in both cases. “Classical” nondividing persister cells have been implicated in treatment failure both in cancer and in microbial infections and are thought to provide a reservoir for subsequent relapse events.In the last 20 years, a new class of cancer drugs, called targeted therapies, have emerged and revolutionized patient care. Unlike chemotherapies or antibiotics, these drugs do not target proliferating cell per se but rather act on specific molecular targets associated with cancer. For example, some targeted therapies target proteins that are more abundant on the surface of cancer cells compared with that of normal cells. While slow proliferation has also been implicated in tolerance in the context of targeted therapy, multiple additional mechanisms are at play, which are not characteristic of microbial persister cells. For instance, oncogene‐targeted therapies are taking advantage of the acquired dependence of a cancer cell on the activity of a single oncogenic gene product. As many oncogenes control cell metabolism (Levine & Puzio‐Kuter, 2010), for example by regulating glucose uptake, drugs that target oncogene addiction can have profound effects on metabolism. In line with this, oncogenic‐persisters, for example, persisters that escape killing by oncogene‐targeted therapies show higher levels of fatty acid oxidation (Oren et al, 2021). This shift away from the “Warburg” glycolytic state into a more mitochondrially active energy production state, which resembles non‐transformed cells, might indicate the release from oncogenic addiction. Importantly, this shift does not lead to overall lower metabolic activity and in some cases might even allow persisters that were arrested to resume cell cycle in the presence of a drug. This high modularity is possible in cancer cells as they can, under certain conditions, tap into a vast space of cellular states that reflect different tissues and developmental trajectories. Cancer persister cell plasticity is perhaps best exemplified by phenotypic transformation from non‐small‐cell lung adenocarcinoma to small‐cell lung cancer upon prolonged treatment with EGFR inhibitors (Shaurova et al, 2020). Such lineage switching accounts for up to 14% of acquired resistance to EGFR‐targeted therapy. Clinical data of relapsed patients strongly support the hypothesis that this transformation happens via persister cells that were able to withstand EGFR therapy. Taken together, these observations show that cancer persister cells can circumvent oncogenic withdrawal by adopting alternative cell states. Notably, these changes do not necessarily require any genetic alteration and in theory can be reversible and potentially mediated by microenvironment signaling.The most recent addition to the cancer‐fighting arsenal are immunotherapies designed to boost immune responses. Immune‐persisters, cells that can evade immune response, have been reported in multiple cancer types and are thought to underlie the late relapse frequently observed in patients (Shen et al, 2020). While tumor dormancy might play a role in this context as well, it is interesting to note that immune evasion can be achieved by modulating immune checkpoint molecules without any need to suppress cell proliferation. Furthermore, in the case of CAR T‐cell therapy, a class of immunotherapy that is based on revamped T cells, persistence might be viewed as a dynamic cell‐to‐cell communication process. It was shown that to elicit killing a cancer cell has to have multiple interactions with a T cell (Weigelin et al, 2021). This multihit sequential process that can take more than an hour in vivo may allow cancer cells to modulate the cytotoxic T cell in a way that would favor their persistence. Hence, understanding what underlies T‐cell phenotypes might as be as important as studying the cancer persister cells they are targeting.The holy grail of the persister filed is finding ways to target these drug‐tolerant cells in a manner that would prevent disease recurrence. However, given at least three classes of persisters have been already reported, and more are expected to arise as we continue to expand our therapeutic toolbox, would it even be possible to implement a single approach to eliminate them? Studies that searched for a magic bullet that could eliminate persister cells were largely based on the hope that persister cells would be less heterogenous than the drug‐naïve cell population they were derived from (Cabanos & Hata, 2021; Hangauer et al, 2017). If such convergence on similar cell states exists upon treatment, it simplifies the need to combine multiple drugs to eliminate the entire cell population. Unfortunately, it seems that persister cells can come in multiple forms and that distinct persister phenotypes may coexist in a single tumor. The major drivers of this heterogeneity currently remain unclear and may include tumor lineage, treatment type, or a combination of both. Moreover, it is unknown if the heterogeneity in persister phenotypes can be predicated based on the drug‐naïve population and how these diverse persister fates are associated with clinical outcomes. Understanding persister heterogeneity is critical as the simplistic approach of trying to eliminate as many persister cells as possible, assumes that all cells are equally pathogenic, which might not be the case if only a subset of them are able to contribute to relapse. Furthermore, persister cells might differ in their aptitude to give rise to cells that harbor a resistance‐mediating mutation. Such differences in evolvability must be considered when weighing possible treatments. Answering these questions would be key to devising effective therapeutic approaches to eliminate persister cells. In the last century, the study of microbial persistence had provided important insights into how to fight infections. Hopefully, in the years to come, we will build upon this valuable knowledge foundation and expend it to devise better ways to fight cancer.     

Measuring how two proteins affect each other's net charge in a crowded environment

Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein''s charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester‐Staudinger pairs) can be used to mimic crowding by linking two non‐interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine‐acyl “protein charge ladders” and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Z _monomer = −0.43 ± 0.01) and α‐lactalbumin (Z _monomer = −4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = −0.04 ± 0.09 upon crowding by this pair (Z _dimer = −5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.     

Fossil Humankind and Other Anthropoid Primates of China

More than 70 sites have yielded human fossils in China. They are attributed to Homo sapiens erectus and Homo sapiens sapiens. The earliest one is possibly about 1.7 Ma. A series of common morphological features, including shovel-shaped incisors and flatness of the face, characterize them. There is a morphological mosaic between H. s. erectus and H. s. sapiens in China. The existence of common features and the morphological mosaic suggest continuity of human evolution in China. That there are a few features which are more commonly seen in the Neanderthal lineage, occurring in a few Chinese fossil skulls, probably suggests gene flow between China and the West. Based on them, in 1998 I proposed an hypothesis—continuity with hybridization—for human evolution in China. The hypothesis is supported by paleolithic archeology, and it supports the multiregional evolution hypothesis of modern human origins. The anatomically modern humans of East Asia originated most probably in China. Although some nonhuman anthropoid primates of China—Gigantopithecus, Sivapithecus, Ramapithecus and Lufengpithecus—have been suggested as the direct ancestors of human beings, the discovery of more specimens and further studies do not support these suggestions. Therefore, it is most probable that the transition between apes and humans did not occur in China.     

Parkin drives pS65‐Ub turnover independently of canonical autophagy in Drosophila

Parkinson''s disease‐related proteins, PINK1 and Parkin, act in a common pathway to maintain mitochondrial quality control. While the PINK1‐Parkin pathway can promote autophagic mitochondrial turnover (mitophagy) following mitochondrial toxification in cell culture, alternative quality control pathways are suggested. To analyse the mechanisms by which the PINK1–Parkin pathway operates in vivo, we developed methods to detect Ser65‐phosphorylated ubiquitin (pS65‐Ub) in Drosophila. Exposure to the oxidant paraquat led to robust, Pink1‐dependent pS65‐Ub production, while pS65‐Ub accumulates in unstimulated parkin‐null flies, consistent with blocked degradation. Additionally, we show that pS65‐Ub specifically accumulates on disrupted mitochondria in vivo. Depletion of the core autophagy proteins Atg1, Atg5 and Atg8a did not cause pS65‐Ub accumulation to the same extent as loss of parkin, and overexpression of parkin promoted turnover of both basal and paraquat‐induced pS65‐Ub in an Atg5‐null background. Thus, we have established that pS65‐Ub immunodetection can be used to analyse Pink1‐Parkin function in vivo as an alternative to reporter constructs. Moreover, our findings suggest that the Pink1‐Parkin pathway can promote mitochondrial turnover independently of canonical autophagy in vivo.     

Phospholipase D1 promotes cervical cancer progression by activating the RAS pathway

This study aimed to further investigate the effect of PLD1 on the biological characteristics of human cervical cancer (CC) cell line, CASKI and the potential related molecular mechanism. CRISPR/Cas9 genome editing technology was used to knock out the PLD1 gene in CASKI cells. Cell function assays were performed to evaluate the effect of PLD1 on the biological function of CASKI cells in vivo and in vitro. A PLD1‐overexpression rescue experiment in these knockout cells was performed to further confirm its function. Two PLD1‐knockout CASKI cell lines (named PC‐11 and PC‐40, which carried the ins1/del4 mutation and del1/del2/ins1 mutation, respectively), were constructed by CRISPR/Cas9. PLD1 was overexpressed in these knockout cells (named PC11‐PLD1 and PC40‐PLD1 cells), which rescued the expression of PLD1 by approximately 71.33% and 74.54%, respectively. In vivo, the cell function assay results revealed that compared with wild‐type (WT)‐CASKI cells, the ability of PC‐11 and PC‐40 cells to proliferate, invade and migrate was significantly inhibited. The expression of H‐Ras and phosphorylation of Erk1/2 (p‐Erk1/2) was decreased in PC‐11 and PC‐40 cells compared with WT‐CASKI cells. PC‐11 and PC‐40 cells could sensitize CASKI cells to cisplatin. More importantly, the proliferation, migration and invasion of PC11‐PLD1 and PC40‐PLD1 cells with PLD1 overexpression were significantly improved compared with those of the two types of PLD1 knockout cells. The sensitivity to cisplatin was decreased in PC11‐PLD1 and PC40‐PLD1 cells compared with PC‐11 and PC‐40 cells. In vivo, in the PC‐11 and PC‐40 tumour groups, tumour growth was significantly inhibited and tumour weight (0.95 ± 0.27 g and 0.66 ± 0.43 g vs. 1.59 ± 0.67 g, p = 0.0313 and 0.0108) and volume (1069.41 ± 393.84 and 1077.72 mm³ ± 815.07 vs. 2142.94 ± 577.37 mm³, p = 0.0153 and 0.0128) were significantly reduced compared to those in the WT‐CASKI group. Tumour differentiation of the PC‐11 and PC40 cells was significantly better than that of the WT‐CASKI cells. The immunohistochemistry results confirmed that the expression of H‐Ras and p‐Erk1/2 was decreased in PC‐11 and PC‐40 tumour tissues compared with WT‐CASKI tumour tissues. PLD1 promotes CC progression by activating the RAS pathway. Inhibition of PLD1 may serve as an attractive therapeutic modality for CC.     

The Neanderthal lower arm

Neanderthal forearms have been described as being very powerful. Different individual features in the lower arm bones have been described to distinguish Neanderthals from modern humans. In this study, the overall morphology of the radius and ulna is considered, and morphological differences among Neanderthals, Upper Paleolithic Homo sapiens and recent H. sapiens are described.Comparisons among populations were made using a combination of 3D geometric morphometrics and standard multivariate methods. Comparative material included all available complete radii and ulnae from Neanderthals, early H. sapiens and archaeological and recent human populations, representing a wide geographical and lifestyle range.There are few differences among the populations when features are considered individually. Neanderthals and early H. sapiens fell within the range of modern human variation. When the suite of measurements and shapes were analyzed, differences and similarities became apparent. The Neanderthal radius is more laterally curved, has a more medially placed radial tuberosity, a longer radial neck, a more antero-posteriorly ovoid head and a well-developed proximal interosseous crest. The Neanderthal ulna has a more anterior facing trochlear notch, a lower M. brachialis insertion, larger relative mid-shaft size and a more medio-lateral and antero-posterior sinusoidal shaft. The Neanderthal lower arm morphology reflects a strong cold-adapted short forearm. The forearms of H. sapiens are less powerful in pronation and supination. Many differences between Neanderthals and H. sapiens can be explained as a secondary consequence of the hyper-polar body proportions of the Neanderthals, but also as retentions of the primitive condition of other hominoids.     

Protein yoga: Conformational versatility of the Hemolysin II C‐terminal domain detailed by NMR structures for multiple states

The C‐terminal domain of Bacillus cereus hemolysin II (HlyIIC), stabilizes the trans‐membrane‐pore formed by the HlyII toxin and may aid in target cell recognition. Initial efforts to determine the NMR structure of HlyIIC were hampered by cis/trans isomerization about the single proline at position 405 that leads to doubling of NMR resonances. We used the mutant P405M‐HlyIIC that eliminates the cis proline to determine the NMR structure of the domain, which revealed a novel fold. Here, we extend earlier studies to the NMR structure determination of the cis and trans states of WT‐HlyIIC that exist simultaneously in solution. The primary structural differences between the cis and trans states are in the loop that contains P405, and structurally adjacent loops. Thermodynamic linkage analysis shows that at 25 C the cis proline, which already has a large fraction of 20% in the unfolded protein, increases to 50% in the folded state due to coupling with the global stability of the domain. The P405M or P405A substitutions eliminate heterogeneity due to proline isomerization but lead to the formation of a new dimeric species. The NMR structure of the dimer shows that it is formed through domain‐swapping of strand β5, the last segment of secondary structure following P405. The presence of P405 in WT‐HlyIIC strongly disfavors the dimer compared to the P405M‐HlyIIC or P405A‐HlyIIC mutants. The WT proline may thus act as a “gatekeeper,” warding off aggregative misfolding.     

An alternative miRISC targets a cancer‐associated coding sequence mutation in FOXL2

The authors note that P values presented in the original Fig 1A and Appendix Fig S1A were not assessed using a proper statistical analysis method. In contrast to the initially employed two‐group t‐test, a one‐sample one‐tailed t‐test is appropriate here, as the basic null hypothesis is that the proportion of MT FOXL2 mRNA in each AGCT patient is lower than WT {H ₀: WT(%) > MT(%) }. New p values are presented in the corrected Fig 1A and Appendix Fig S1A, which are P < 0.00001 and P < 0.05, respectively. These revised P values did not affect the conclusion drawn.     

Microtubules are not required to generate a nascent axon in embryonic spinal neurons in vivo

Our understanding of the cell behaviours and cytoskeletal requirements of axon formation is largely derived from in vitro models but how these relate to axon formation in vivo is not clear. In vitro, neurons progress through a well‐defined multineurite stage to form an axon and both actin and microtubules cooperate to drive the first steps in neurite and axon morphogenesis. However, these steps are not recapitulated in vivo, and it is not clear whether the underlying cell biological mechanisms may differ also. Here, we investigate the mechanisms that regulate axon formation in embryonic zebrafish spinal neurons in vivo. We find microtubule organising centres are located distant from the site of axon initiation, and microtubule plus‐ends are not enriched in the axon during axon initiation. Focal F‐actin accumulation precedes axon formation, and we find that nocodazole‐treated neurons with no detectable microtubules are still able to form nascent axonal protrusions that are approximately 10‐μm long, dilated and relatively long‐lived. We suggest spinal axon formation in vivo is fundamentally different from axon formation in in vitro models.     

Co‐production of biofuel,bioplastics and biochemicals during extended fermentation of Halomonas bluephagenesis

Halomonas bluephagenesis TD1.0 was engineered to produce the biofuel propane, bioplastic poly‐3‐hydroxybutyrate (PHB), and biochemicals mandelate and hydroxymandelate in a single, semi‐continuous batch fermentation under non‐sterile conditions. Multi‐product separation was achieved by segregation of the headspace gas (propane), fermentation broth ([hydroxy]mandelate) and cellular biomass (PHB). Engineering was performed by incorporating the genes encoding fatty acid photodecarboxylase (CvFAP) and hydroxymandelic acid synthase (SyHMAS) into a H. bluephagenesis hmgCAB cassette knockout to channel flux towards (hydroxy)mandelate. Design of Experiment strategies were coupled with fermentation trials to simultaneously optimize each product. Propane and mandelate titres were the highest reported for H. bluephagenesis (62 g/gDCW and 71 ± 10 mg/L respectively) with PHB titres (69% g/gDCW) comparable to other published studies. This proof‐of‐concept achievement of four easily separated products within one fermentation is a novel achievement probing the versatility of biotechnology, further elevating H. bluephagenesis as a Next Generation Industrial Biotechnology (NGIB) chassis by producing highly valued products at a reduced cost.

Halomonas bluephagenesis TD1.0 was engineered to generate multiple products propane, poly‐3‐hydroxybutyrate and (hydroxy)mandate. These compounds are easily purified due to their location in the gas, phase, cell pellet and culture supernatant, respectively. This proof of principle study shows the potential application of multi‐product biosynthesis within an industrially relevant host as a route to renewable and sustainable bio manufacturing.     

Trigonid crests expression in Atapuerca-Sima de los Huesos lower molars: Internal and external morphological expression and evolutionary inferences

Trigonid crest patterning in lower molars is distinctive among Late Pleistocene hominins such as Homo neanderthalensis, fossil Homo sapiens and modern humans. In this paper, we present an examination of trigonid crest patterning in the Middle Pleistocene permanent lower molar sample (n = 62) of Homo heidelbergensis from Sima de los Huesos (SH). Crest expression was assessed from 3D models of the enamel and the dentine surfaces that were produced using micro-computed tomography (microCT). The aims of our analysis are to: 1) characterize the pattern of trigonid crest expression at the outer enamel and enamel-dentine junction surfaces (OES and EDJ) of the SH sample, 2) evaluate the concordance of expression between both surfaces, and 3) place trigonid crest variation in the SH sample into a phylogenetic context. Our results reveal a greater variability in the expression of trigonid crests at the EDJ (14 types) compared to the OES (4 types). Despite this variability, in almost all cases the expression of a continuous mid-trigonid or distal crest at the OES corresponds with the expression of a continuous mesial/mid-trigonid or distal trigonid crest, respectively, at the EDJ. Thus, it is possible to predict the type of trigonid crest pattern that would be at the OES in the case of partially worn teeth. Our study points to increased variability in trigonid crest expression in M₃s compared to M₁s and M₂s. Moreover, our analysis reveals that the SH sample matches broadly the trigonid crest patterns displayed by H. neanderthalensis and differs from those exhibited by H. sapiens, particularly in the almost constant expression of a continuous middle trigonid crest at the EDJ. However, SH hominins also exhibit patterns that have not been reported in H. neanderthalensis and H. sapiens samples. Other aspects of the variability of the trigonid crest expression at the dentine are presented and discussed.